agilent qc tool (v1.0)

Agilent QC Tool (v1.0)

User Guide

QC Tool User Guide (v1.0) Copyright 2006, Agilent Technologies 1

Contents

1 Overview ........................................................................................................... 3

2 Objective ........................................................................................................... 3

3 Installation ........................................................................................................ 4

4 Loading Data .................................................................................................... 5

5 Associate Annotations...................................................................................... 8 Export-All Method............................................................................................. 8 Export-Subset Method ..................................................................................... 11 Generate-New Method..................................................................................... 11

6 Defining Queries............................................................................................. 11

7 Defining Metric Sets and Thresholds ........................................................... 16 7.1 Defining Metric Sets ............................................................................. 17 7.2 Defining Metrics ................................................................................... 17 7.3 Set Thresholds....................................................................................... 23 7.4 Export and Import Metric Sets.............................................................. 25 7.5 Setting the Mandatory and In Range Evaluation status for metrics...... 26 7.6 Removing and duplicating the metric-sets............................................ 26 7.7 Removing metrics ................................................................................. 27

8 Defining a QC Chart...................................................................................... 27 Color by In\Out of Range................................................................................. 28 ShapeBy and ColorBy options......................................................................... 28 Viewing the QC Chart...................................................................................... 28 Using the QC Chart View Options .................................................................. 29

9 Extraction Queries and QC Charts Pane .................................................... 30 Extraction Queries Pane................................................................................... 30 QC Charts Pane ................................................................................................ 31

10 Extraction Results Pane................................................................................. 31

11 Reset and Remove Database operations ...................................................... 32

12 Application Themes ....................................................................................... 33

13 Use of Metric sets in Feature Extraction...................................................... 33

14 Overview of Feature Extraction & QC Chart Tool Connection................ 35

15 Feature Extraction FEParameter fields used in QC Chart Tool............... 36


1 Overview The QC Chart tool is a desktop application that accumulates, aggregates and analyzes summary statistics from Feature Extraction output files and optional annotation files for the purpose of monitoring microarray processing performance. The data is housed in a relational database from which queries can be generated and saved to subset the data into user-defined logical groupings such as by experiment, by batch, or by date of processing. Using the data, metrics can be generated that monitor aspects of the microarray processing workflow. Metric sets can be formed that combine metrics that monitor different aspects of microarray processing. With metric sets, you can plot graphically the results from historical data and generate thresholds for the metrics that are appropriate for your experimental conditions and processing environment. The metric sets and thresholds can be used in the QC Chart tool on a regular basis to monitor processing performance. They can also be imported to Feature Extraction software to monitor each array and batch as it is processed. The QC Chart Tool is meant to be used in a production environment where:

1. Biological samples are similar 2. Microarray processing protocols are identical 3. Monitoring run-to-run consistency is an important goal

The QC Chart Tool v1.0 is provided as an optional accessory to Feature Extraction (FE) 9.1. The software must be installed on a computer with FE 9.1 already functionally installed but does not require a separate license to operate. Agilent provides the software “AS IS” and any express or implied warranties, including, but not limited to any implied warranties of merchantability, satisfactory quality, reasonable care and skill, and fitness for a particular purpose are expressly disclaimed. For the most recent information on the QC Chart Tool, please go to the Web site: http://www.agilent.com/chem/FEQCMetrics This web site will contain updates to the software and this manual as well as example metric sets as they become available.

2 Objective The QC Chart utility provides the ability to determine the quality of extractions. Currently Feature Extraction software can run a batch of arrays generating a batch summary and a quality control report (QC Report) per microarray. In order to ensure the quality of the array, you should check the QC report of each array. To have a summary of quality of batch extractions, the QC Chart Tool is introduced. This tool will allow you to define quality metrics, apply those metric criteria to extraction data, and verify quality metrics through QC Charts.


http://www.agilent.com/chem/FEQCMetrics

This tool has the following features (see Appendix 1 for overview): • Ability to have all extractions in a central repository • Ability to share central repository • Ability to annotate extractions with custom annotation. • Ability to filter extractions by defining queries • Define metrics to monitor quality • Define thresholds for metrics to check performance/quality of extraction • Define metric sets as a set of metrics (with or without thresholds) • Define a Quality chart (“QC Chart”) by defining query filters, metric set, and

chart formatting on extraction set • Export QC Chart data for further use • Export metric set for use in FE • Evaluate quality of micro-array scans in a FE batch against a given metric set • Create a Batch summary chart from each FE batch for a given metric set • Create a QC Chart of extractions from an FE batch for a given metric set

3 Installation The first step in using the QC Chart tool is setting up the central repository or a database. The QC Chart tool operates by storing all the data in this repository so all the menus except the ‘Configure Database Settings’ menu are disabled as shown below.

The database is configured as follows: 1. Click on ‘Configure Database Settings’ menu or just press Ctrl + D. 2. The following dialog is launched


3. A ‘QC Chart Database Settings’ dialog is launched. 4. In the ‘SQL Server Instance Name’ edit-box type in the machine name along with

the database that FE uses. E.g.: ps0546\AGTFEDB where ps0546 is the machine name. For the users it will be <machine_name>\AGTFEDB. NOTE: To find out the machine name; Launch ‘Start Run’ and type in “cmd”. At the command prompt type ‘hostname’. Alternatively, one can find the SQL server name in FE by choosing the menu: Help>About:

5. Copy the name after “SERVER=” and before “;DATABASE” and past into the

“SQL Server Instance Name” field of the QC Chart configuration UI.

6. If the tool is launched for the first time, choose the ‘Create new database’ radio button. In the ‘Specify folder name to store database files’ hit the Browse button and choose the default database path.

7. In the User Info frame, type ‘sa’ in the user-name edit box and ‘welcome’ in

the password edit box. 8. If the user needs to map the tool to some other user’s database, re-launch

the DB configuration dialog by pressing Ctrl+D or choosing ‘Configure Database Settings’ and change the <machine_name> field in the ‘SQL Server Instance Name’ edit box to the appropriate machine and hit the ‘Done’ button. Make sure that the ‘Map to existing Database’ radio button is selected.

9. Hit the ‘Done’ button to save the configuration.

If the database is properly set all the relevant menus will be enabled in the tool.

4 Loading Data


The QC Chart tool needs extractions imported in its database to create meaningful metrics and thresholds. Loading the tool with extractions consists of extracting the Stats and FEParameter data from the output text files of FE. Importing the FE output text files can be done either by selecting the files individually or by specifying the base folder for recursively importing all the FE text files within all the sub-folders. To import the FE text files by individual selection, choose ‘File Import Files FE Files…’ or press ‘Ctrl + F’.

The ‘Browse FE files’ dialog will be launched which will allow the user to select FE text files individually as shown below. Hit the ‘Open’ button to import the extraction-data from the selected files.

To import files recursively specify the base folder by choosing ‘File Import Files Recursively’ from the menu or by pressing ‘Ctrl + R’.

The following ‘Browse for Folder’ dialog will be displayed as shown below.


Choose ‘OK’ to start importing. If there are a large number of files in the sub-folders this operation may take some time. It takes about 15-20 minutes to import 2000 FE files.

Sometimes the files that are chosen may not be FE output text files. In such cases, the following dialog displays all the files that the tool classified as invalid in a list box as shown below.

Choose “OK” and the import will continue. The import process creates a “row” or “record” for each unique extraction. If a barcode has been extracted with various FE protocols, these will result in unique


records, as the extraction name is created from both the barcode and the name of the protocol. Two types of data are imported: - All Stats fields from the extraction - Selected FEParameters fields are also imported to aide the user in defining queries of the extractions (see Chapter 15 for a list of imported parameter fields).

5 Associate Annotations Users can create annotations for the extractions that exist in the QC Tool repository and import the annotations with the tool. Purpose: annotation associated with an extraction can be used to filter for that extraction in queries, discussed below. The annotation can also be used to organize data in QC charts produced by the QC Chart Tool; for instance, to sort extractions, or to indicate different subsets of extractions by color-coding or by shape-coding. The user can add annotations by one of three different methods,

1) Exporting all database information, editing and re-importing 2) Exporting a subset of the database information, editing and re-importing 3) Generating a new tab-delimited text file containing the annotations

Each method is described below

Export-All Method 1. Once extractions are loaded into the QC Tool repository, all barcodes (and

their associated FEParams and Stats) can be exported in the QC tool by choosing ‘File Export Database’ or Ctrl + A. This method will result in the export of every extraction in the repository.

2. Custom annotations can be entered by opening the text file in a program such as Microsoft Excel. Add additional custom columns (with descriptive column header names in the first row) and array annotations within those columns as desired. Column header names must not contain any space characters. It is imperative that the ‘BarCode’ column is left exactly as exported, or the re-importation into the tool will not work. See the example below:


BarCode Project Experiment RedSample GreenSample Polarity Comments Stringency251209751852 STG_1 GE1_Human_June06 h1 h2 1 v4 251209751871 STG_1 GE1_Human_June06 h1 h2 1 v4 251209751873 STG_1 GE1_Human_June06 h1 h2 1 re-scanned v4 251209751882 STG_1 GE1_Human_June06 h2 h1 -1 v4 251209751884 STG_1 GE1_Human_June06 h2 h1 -1 v4 251209751886 STG_1 GE1_Human_June06 h2 h1 -1 v4 251269421651 STG_1 GE2_Mouse_May06 m1 m2 1 trainee Legacy 251269421653 STG_1 GE2_Mouse_May06 m1 m2 1 trainee Legacy 251269421655 STG_1 GE2_Mouse_May06 m2 m1 -1 Legacy 251269421658 STG_1 GE2_Mouse_May06 m2 m1 -1 Legacy 251209751887 CGH_prep Compare 2 preps k1 k2 1 v3 251209751890 CGH_prep Compare 2 preps k1 k2 1 v3

3. Delete all columns (FEParameters and Stats) other than “BarCode” and user-

added annotations before re-import into the tool.

4. Confirm that Excel has not changed the formatting of the BarCode column. If the formatting has changed, change it back as described below.

The BarCode format needs to be modified to allow correct re-import into the QC Tool. To do this, highlight the BarCode column,

then choose the Excel menu item: Format>Cells>Number and choose Category = Number and choose “Decimal places” = 0, as in the following screen shot.


Now, the BarCodes will be in the correct format for re-import into the QC Chart tool.

5. After creating the annotations save the file in tab-delimited-text (TDT) format. Excel may prompt with the following screen:


6. Choose “Yes” 7. Once the annotations are created and saved in TDT format, they can be

imported into the tool by choosing ‘File Import Files Annotated Extractions’ or Ctrl + E.

Export-Subset Method A QC repository may consist of extractions that already have been annotated, as described above. If new extractions are added, the user can create a query to identify the subset of barcodes which have no annotation, and then just export those for annotation. This method will be shown in greater detail below in Section 6 “Defining Queries”, Example 3. Note: as discussed in the Export-All method, all Stats and FEParameter columns need to be deleted before re-importation into the QC Chart Tool, and the BarCode field needs to be correctly formatted. The annotation file should only have the BarCode and any user-added annotation.

Generate-New Method If there are only a few barcodes to be annotated, then the user can open a blank Excel worksheet and type in the BarCode numbers exactly as they appear in the QC repository. Proceed as in steps 2, 5, 6, and 7 from the Export-All method above.

6 Defining Queries The QC Chart tool supports a Query Builder that allows the user to select a subset of the extractions among the ones available in the QC Chart tool repository. Purpose: A query is used to define a subset of extractions that define a representative data set for use in metric and threshold development. The representative data set should optimally contain data only from similar biological samples processed under identical conditions. Use of metrics and thresholds are discussed in Section 7, “Defining Metric Sets and Thresholds”. A subset of extractions may be defined by specific FEParameter fields, or by user-added annotation fields. To define queries launch the query builder by choosing ‘View Extraction Query Builder’, by pressing Ctrl + Q, or by right-clicking in the “Extractions” pane and choosing “Add New”.


Example 1: To choose all 1-Color extractions choose the ‘Color Mode’ from the “Column name” drop down list. In the “Operator” drop-down list choose “=” and then in the right-most box, choose ‘1-Color’. Then hit ‘Add’. The SQL for that query will be displayed (e.g. “ColorMode = 0”. Click the ‘Verify’ button to ensure that the query is valid. If the query is valid the ‘Show Results and Save’ buttons will be enabled. Clicking the ‘Show Results’ button will display the results for the current query. The user can save the query with any user-defined name. The following screenshot shows this first example.

Example 2: The user can create composite SQL queries by combining then query clause with ‘AND’, ‘OR’ and ‘NOT’ operators. The query clauses can be grouped together by adding braces. The braces buttons are enabled after the user clicks on a query clause in the list box. An example of choosing all 2-color extractions that are also GeneExpression (e.g. Filtering out 1-color and CGH arrays) is showed below: Choose 2-color extractions:


Choose “AND” button then choose Gene expression extractions:

Choose “Verify”:


Now, the user can choose “Show Results” to see the returned set of extractions. If this is a query that should be saved, then enter desired name (e.g. “GE2”) and choose “Save”:


Example 3: As discussed above, one may wish to find all barcodes that have not yet been annotated. One can do this by filtering on a user-added field, such as “Project” and finding records where this field is null as shown below.

Choose “Add”, “Verify” and enter name to save:


The query now shows in the extraction pane. Selecting it will display all records that have no “Project” annotations, as shown below.

Once the results of the Null_Project are displayed (e.g. 8 records in above example), these results can be exported by right-clicking the name of the query and choosing “Export results to file…”. Now, the file can be opened and annotated as described in Section 5 “Associate Annotations”, “Method 1).

7 Defining Metric Sets and Thresholds Purpose: Metrics are defined in order for the user to follow desired statistical values across a set of extractions. These metrics can be associated in a metric set. In addition, the user can use this tool to specify thresholds for each of the metrics. This ‘Configure Metrics and Thresholds’ dialog implements the concepts of defining a metric set and thresholds. This dialog is accessible through ‘Configure Metrics’ menu or pressing ‘Ctrl + M’.

The ‘Configure Metrics and Thresholds’ dialog is shown below…


7.1 Defining Metric Sets A metric-set is a collection of one or more metrics and an associated query common to all the metrics. To add a metric set, right click on the white space below the ‘Metric Sets’ label. Then choose ‘Add Set’. A new pop-up appears asking the metric-set name. Choose any suitable alphanumeric name and hit OK.

7.2 Defining Metrics A new metric can be defined by choosing ‘Add New…’ from the Metric drop-down list in the ‘Configure Metrics and Thresholds’ dialog. The following ‘Add Metric’ dialog is launched …


The drop down list shows all available metrics from the FE Stats table output. The user can select one of these calculations, or may define a new metric as an expression. A metric expression can be created using the metric columns and operators as shown above. For example, FE calculates a slope for the eQC spike-ins (observed vs. expected Log Ratio). Depending upon the hybridization, this spike-in mixture may be present as “+1” or “-1” polarity. If it is “-1”, then any threshold that is set (e.g. Slope > 0.85), will not pass. Thus the user needs to make a derivative metric by taking the absolute of the slope. To do this, first choose the “Abs” function in the dialog. This yields “Abs( “ in the “Metric Calculation” pane, as shown below:


Now, from the drop down list, choose the statistic “eQCObsVsExpLRSlope”, choose “Add”, then choose “ )” to finish the expression, as seen below:


Once the metric expression is created, it needs to be validated: choose “Validate” button. After the expression passes the validation, the “Save” button is enabled. Choose a name to save, as shown below:


The saved metric will now appear in the ‘Metric drop-down’ in the ‘Configure Metrics and Thresholds’ dialog.


To associate a metric with a metric set, first choose the desired metric from the drop down list. Next, a query needs to be associated with the metric set. This query will filter for the appropriate extractions from your database, so that just the data from the queried extractions will be used in calculation of various statistical summary values that may be used in setting thresholds, described in the next section. For this example, the “Extraction Query” chosen from the drop down list is “GE2”, as the metric set will be used with two-color Gene Expression extractions:

Now, the metric needs to be associated with the desired metric set. Highlight the appropriate metric set, e.g. “Test_1”, then, then choose “<< Add/Update Metric” button. Now, when the “Test_1” metric set is expanded (e.g. choose “+” button next to “Test_1” name), the associated metric, “Abs_eQCSlope”, is shown:


To assign additional metrics to this metric set, one repeats the above steps, with one exception. After choosing desired metric, one has to choose the same extraction query, e.g. “GE2”, as chosen for first metric. That is, all metrics in a metric set need to be associated with the same extraction query.

7.3 Set Thresholds If the user wants to associate a threshold with a given metric, this can be done at the same time that the metric is associated with a metric set, or can be done after the association. Example 1: the metric “Abs_eQCSlope” has been associated with the metric set “Test_1”, as described above. Select “Test_1” metric set and select the metric beneath it, “Abs_eQCSlope”. The next step is to decide what type of threshold will be associated with the metric, selecting from the following four radio buttons…

1) None. 2) Upper Limit. 3) Range. 4) Lower Limit.

The tab-control on the right contains the different calculation types that can be used to set thresholds. They are Manual Limits, Standard Limits, Robust Limits and Percentile Limits. Clicking on the tabs displays the relevant calculations and their limits. The edit boxes accept floating point constants that allow the user to modify the default limits. After the user is done with setting the limits, he\she can use the ‘Add\Update button’ below in the ‘Configure Metrics and Thresholds’ dialog to add the chosen metric along with its limits to the highlighted\selected metric-set. If the metric is already present then it will be updated with the new limits. For this


example, the threshold type for the slope will be a “Lower Limit” type, since we want to flag extractions that have an absolute slope lower than a user-determined value. This threshold value will not be calculated from the extractions defined in the extraction query, but will be manually set to “0.85”, as shown below:

Choose “<< Add/Update Metric” button to associate this threshold with this metric in this metric set. Example 2: Choose the metric, “gNegCtrlSDevBGSubSig”; set “Extraction Query” = “GE2”; select “Threshold Type” = “Upper Limit” (since we wish to flag extractions with a high SD of Negative Control BkSubtractedSignals); select “Standard” type of calculation with a constant of “3” (multiplier of SD). This then calculates the statistics of the gNegCtrlSDevBGSubSig values of all extractions that are in the “GE2” extraction query set. For this example, calculations include the mean and the standard deviation. An upper limit is then set as mean + 3*SD, which is shown to be = 18.79 in this example:


Choose “<< Add/Update Metric” button to associate this threshold with this metric in this metric set. If one chooses the “Robust” type of calculation, then the median and IQR (inter-quartile range) is calculated. Using the IQR, the robust equivalent of SD is also calculated. The ‘Configure Metrics and Thresholds’ dialog has two radio buttons: Display Current Values and Display Saved Values. This is useful when the user imports some more extractions after the metric has been created. The ‘Saved’ option will display the old threshold limits and the ‘Current’ option will display the limits as per the latest data which may differ from the previously saved limits.

7.4 Export and Import Metric Sets The created metric sets can be exported to an XML file and re-imported in the QC Chart tool as well as FE. This is accomplished by choosing ‘Export Metric Set…’ menu after highlighting the relevant top-level node in the metric-set tree and right-clicking. The use of an exported metric set in FE will be discussed below. In addition, the use can choose ‘Import Metric Set…’ to import metric-set XML files. For example, Agilent may post metric sets on the web for download by users. The user can import a given metric set by right-clicking anywhere on the Metric Set pane and browsing to the appropriate metric set. Upon import, you may see this dialog:


Choose “Yes”. This metric set can be duplicated and modified by the user. For instance, the user can associate this metric set with a query, add or remove metrics, add thresholds, etc, as discussed above.

7.5 Setting the Mandatory and In Range Evaluation status for metrics. Highlight the relevant metric set in the metric-set tree on the ‘Configure Metrics and Thresholds’ dialog, right-click, and then choose ‘View Thresholds…’ from the right click menu. The following dialog is displayed…

To define an extraction evaluation: check the metrics that need to be mandatory. For an extraction to “pass” a metric set with any “mandatory” type of metrics, each of the mandatory metrics must be in the threshold range. Type-in the total number of metrics that need to be within range in the enabled edit-box provided and save the settings. For the above example, there are two metrics that are mandatory to be in range. The third metric is not required to be in range.

7.6 Removing and duplicating the metric-sets.


Right click on the relevant metric-set in the metric-set tree on the ‘Configure Metrics and Thresholds’ dialog. Choose ‘Remove Set’ from the right-click menu to remove the metric set. NOTE: If the metric set is associated with any chart then it will still remain in the system. The semantics of metric-set require that a query that is common to all the metrics within it be assigned along with the metrics. But in some cases the user may need to create the metrics without associating any query with the metric-set. The ‘Duplicate Set’ option from the right-click menu will be helpful in such case. The user can create the duplicate with ‘none’ as query and associate a query later. The following dialog shows the same…

The user can also associate other queries if he\she wished to.

7.7 Removing metrics Select on a metric within a metric set and choose the “Remove Metric >>” button on the ‘Configure Metrics and Thresholds’ dialog to remove the metric from just that metric set. If you wish to remove a metric globally, then select that metric from the drop down list of the ‘Configure Metrics and Thresholds’ dialog and then select the “X” button to the right of that metric. This will remove that metric from any metric set that had that metric associated.

8 Defining a QC Chart A chart can be drawn on a metric-set for a chosen query. The QC chart can be defined in the ‘QC Chart’ dialog accessible through ‘Configure QC Chart…’ menu or by pressing ‘Ctrl + W’. On this dialog the user can choose the Metric-Set from the ‘Metric-Set drop-down’ and the extractions from the ‘Extraction Query drop-down’ on which the associated metric expressions are executed to produce a chart. The ‘Sort by Columns’ pane allows the user to order the points in the chart as per the columns chosen from the drop-down.


Color by In\Out of Range Choosing this mode causes the points on the chart to be color-coded depending on whether the extraction data points fall within the threshold limits or not. The points can be of two colors. The points that are outside the limits will be color-coded in RED and the ones within the limits will be color-coded in ‘BLUE’. All the points are connected by a light-gray line. The ShapeBy and ColorBy columns are disabled if this option is chosen. All points that are within range are of one shape and the ones out of range are the other shape. The ‘Color by in\out of range’ checkbox needs to be checked to use this option.

ShapeBy and ColorBy options In the absence of ‘Color by in\out of range’ option these drop-downs allow the user to tell what shape should the points be grouped into and in what color the points need to appear. For example: ShapeBy: Username and ColorBy: ColorMode creates a chart where all the points that are 1C extractions are of one color and all 2C extractions are of another color. Also, all the extractions that are from a particular user will have same shape relative to a different color for other users. The following is the screenshot of the dialog where the above options can be configured…

Viewing the QC Chart The configured chart can be viewed from the ‘QC Chart’ dialog accessible through ‘Configure QC Chart’ or by pressing Ctrl + W as shown above. Then click the ‘View Chart’ button to launch the ‘QC Chart View for MetricSet’ dialog that contains the configured QC Chart as shown below.


Using the QC Chart View Options Once the ‘QC Chart View for MetricSet’ dialog is launched the dialog will have an ‘Export to File’ button on the left pane that will allow the user to export the data in TDT format. This dialog also sports ‘Copy As Bitmap’, ‘Print’ and ‘Zoom’ buttons.

1. Highlighting the ‘Zoom’ button or the checkbox on the left allows the user to zoom the chart repeatedly. The user needs to double-click on the chart to return to normal view. 2. The ‘Print’ dialog will take the user to the print dialog. 3. ‘Copy as Bitmap’ button copies the chart to clipboard as a bitmap which can be pasted in MS-Word and MS-Paint or in any other appropriate software. 4. ‘Export’ copies the following columns to a TDT file… Ordinal Number ExtractionName InRange MetricName Ismandatory Limits The ‘MetricName Ismandatory Limits’ are repeated as many times as the number of metrics in the metric-sets. A sample output is show in the following screenshot.


Checking the ‘Scrollable’ checkbox makes the X-axis scrollable if the number of data points do not fit within the screen area.

9 Extraction Queries and QC Charts Pane This pane supports two tabs viz:-

1. Extractions. 2. QC Charts.

Extraction Queries Pane This pane supports the operations as shown by the following screenshot…

The ‘Add New’ option is similar to launching the query builder from ‘View Extraction Query Builder’ or by pressing Ctrl + Q.


The ‘Edit Using QueryBuilder’ allows the user to modify an already created query. In this case the query builder is launched with the previously saved query pre-populated. The ‘Delete’ menu deletes the highlighted query from the QC Chart repository. The ‘Execute’ menu executes the query and displays the results in the grid-view on the right. The ‘Rename’ option allows the user to rename the query. The ‘Export Results to File...’ exports the query results to a TDT file.

QC Charts Pane This pane supports the operations as shown by the following screenshot…

The ‘Add New’ menu launches the ‘QC Chart’ dialog which is same as accessing it through the ‘Configure QC Charts’ or by pressing Ctrl + W. The ‘Show Chart Configuration’ option launches the same dialog as of above but will have the saved configurations reflected in the dialog. This option is useful if the user wants to make minor changes to the existing configurations and save it with a different name. The ‘Delete’ menu deleted the saved chart along with its configuration. The metric-sets and queries associated however remain in the QC Chart repository. The ‘View Chart’ menu launches the ‘QC Chart View for MetricSet’ dialog which is the same as clicking on ‘View Chart’ on the ‘QC Chart’ dialog after launching it with the saved configuration. The ‘Rename’ menu will rename the chart.

10 Extraction Results Pane The extractions loaded into the QC Chart tool repository are displayed in the form of a grid-view. The following screenshot shows the same…


The column-headers appear in the following order… Barcode User Added Annotations FE text Params FE text Stats The following screenshot shows the operation supported by the right-click menu on the grid.

1. The ‘Fit Column to Window’ makes the current column the size of the window. But it doesn’t scroll the column so that it is the only one visible in the screen. This option is used to resize the column to the size of the results pane. 2. The ‘Best Fit Column Sizes’ performs a best-fit for all the columns given the pane size. 3. The ‘Find in Current Column’ finds the text in the current column and highlights the found item. To consecutively find the next matching item this operation has to be repeated. 4. The ‘Find in All Columns’ finds the text in the all the columns and highlights the found item. To consecutively find the next matching item this operation has to be repeated.

11 Reset and Remove Database operations The ‘Reset Database’ accessible through the ‘Options Reset Database’ menu or by pressing Ctrl + T. Executing this option will clear all the data in the QC Chart tool repository. The ‘Remove Database’ accessible through ‘Options Remove Database’ menu deletes the QC Chart database totally. If the user wants to re-use the tool he\she has to configure the database as described in the ‘Configure Application’ section.


12 Application Themes The QC Chart tool can sport three desktop application themes as shown in the below screenshot. The user can check the desired theme for look and feel of their liking.

13 Use of Metric sets in Feature Extraction Purpose: Metric sets can be associated with FE projects to give information to the user for each extraction: - QC Chart showing value of each metric for each extraction - whether metrics are within range (if thresholds are set) - whether extraction is within range (if evaluation metric has been set) As discussed above, you can export a metric set so that it can used by FE. In the FE UI, locate the “QC Metric Set Browser” pane. If it is not visible, choose the menu: View> QC Metric Set Browser. Right-click in the pane and choose “Import” and browse to the desired metric set. After import, double-click on the metric set to see the metrics, thresholds and any mandatory metrics that are defined by this metric set.


Once a metric set has been imported into FE, it is available to be associated with any FE project. To associate a metric set with a project, choose the desired metric set from the drop down box “QC Metric Set” in the “Other” section of the FE “Project Properties” tab:

When this project is run, the metric set will be used to yield the following output:

1. QC Chart: a run-chart type view showing extractions statistics for metrics: a. Chart visible on screen showing all extractions on X-axis with value of

metric on Y-axis. If there are multiple metrics in the metric set, the plots will be stacked.

b. The QC Chart can be printed or saved as text file c. The key showing where barcodes are plotted along the X-axis can also

be printed 2. Project Run Summary: new information

a. If thresholds are associated with the metric set, will show how many metrics were in range for each extraction

b. If an evaluation metric was associated with the metric set, will show how if the extraction is in range, or needs evaluation by the user

3. QC Report: new information a. Header: If thresholds are associated with the metric set, will show how

many metrics were in range for each extraction b. At the bottom of the QC Report, will show a table listing each metric

and the value calculated for that extraction


c. If thresholds are associated with the metric set, will show: i. Value of threshold ii. Color-code which metrics were in range

14 Overview of Feature Extraction & QC Chart Tool Connection

Performance data: median signal intensities, # saturated features, S/N

FE 9.1

Tabtextdata

QCreports

Define Metricsand Thresholds

Run Charting DB

Query and Presentation Capabilities

Metrics and thresholdsappear in FE 9.1

QC reports

Performance data: median signal intensities, # saturated features, S/NPerformance data: median signal intensities, # saturated features, S/N

FE 9.1

Tabtextdata

QCreports

Define Metricsand ThresholdsDefine Metricsand Thresholds

Run Charting DB


Run Charting DB



QC reports


QC reports


15 Feature Extraction FEParameter fields used in QC Chart Tool

BarCode ExtractionName UserName ExtractionTime ComputerName Version ScanFileName PatternName DesignFileName Protocol_Name Protocol_Date Scan_ScannerName Scan_Date QCReportType ColorMode Scan_NumChannels Scan_MicronsPerPixelX Scan_MicronsPerPixelY Grid_Name Grid_Date Grid_NumRows Grid_NumCols Grid_NomSpotWidth Grid_NomSpotHeight


agilent qc tool (v1.0)

Documents