copyright 2000, media cybernetics, l.p. array-pro ® analyzer software

Copyright 2000, Media Cybernetics, L.P.

Array-Pro® Analyzer Software


Problems with Current Array Analysis

• Tedious manual application of grid templates

• Non-reproducibility from one user to another or the same user doing a similar analysis on another sample

• Poor user feedback on image and hybridization quality

• Poor signal/noise performance due to lack of understanding of signal/background


Goals for Array-Pro• Automate grid/spot finding based on our superior knowledge

of image processing; find regular & irregular array spotting• Allow manual setup but let the computer make decisions

whenever possible for reproducibility• Give the user constant feedback in processing and data to aid

their assessment of array and spot quality• Use our experience in image processing to optimize

signal/noise performance• Read existing file formats (mostly TIFF)• Drive confocal microscopes with automation to collect

images


Application Goals

• Ability to generate information from all kinds of arrays – Spotted arrays

– Gene chips (e.g. Affymetrix)

– Membranes (e.g. Clontech Atlas, Research Genetics) • Especially well-suited for gene expression

– Ratios (usually Cy3/Cy5) – Scatter plots, tables, color-coded graphics, etc. to expose gene

expression


Experiment Driven


Spot ID Wizard


Wizard Continued


Auto Grid/Spot Detection Parameters


Advanced Detection


Numerous Measurements/Descriptors


Analysis Options


Labeling


Background Characterization


Information View Definition


ID and Replication


Grid Labeling Options


Data Tables


Statistical Feedback


Data Histograms


Cell Group Information


Scatter Plot


Other Features• Floating windows of information over cells in image

• Label importing

• Definition of groups, including fiducials, background, housekeeping genes, outliers, etc.

• Interactivity of data and graphics

• Working with spots or user-defined groups of spots

• Image & hybridization quality metrics; user weighted

• Scope-Pro as a plug-in module to automate microscope stages

• Database storage


Partnership with Applied Maths

• Array-Pro shares data seamlessly with GeneMaths®

• Can start GeneMaths from Array-Pro and pass

experiment data automatically

• Sophisticated statistical analysis of experimental series data


GeneMaths®

• Standardization of data matrix using offset and scaling functions (averages, Root Mean Square, Standard Deviation)

• Transformation of data matrix (flipping)

• Powerful two-way cluster analysis of rows and columns using a variety of similarity/distance coefficients, and several pair-group clustering methods, Ward, and Neighbor Joining

• Cluster significance indication based on bootstrap techniques

• Very powerful dendrogram layout and visualization tools to facilitate interpretation of analyses of extreme sizes

• Use and display up to 20 database fields both for rows and columns

• Advanced search and select functions based upon database information

• Pattern matching: search for closest matches with specific profiles, average profiles or theoretical profiles

• Single, composite or average profile curve or bar graph plotting with indication of standard deviations

• X-Y plots, time course plots, and scatterplots; 2-D and 3-D Principal Component Analysis and Discriminant Analysis with or without variance

• Advanced Self-Organizing maps (Kohonen maps) of any size with unique presentation and interpretation

tools; Powerful WYSIWYG printing of any result.


GeneMaths®

copyright 2000, media cybernetics, l.p. array-pro ® analyzer software

Documents

media cybernetics

labeling slide

images slide

replication slide

signalbackground slide

gene expression slide

analysis options slide

statistical feedback