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Data Analysis Tools
1. GenePix Pro 5.0 Microarray Analysis Software (Axon Instruments, Inc). Acquires antigen feature intensity data for export into Microsoft Excel.
2. ScanAlyze2 (Michael Eisen's laboratory). Converts images contained in TIF files acquired from scanner into BMP files.
3. Cluster and Treeview (Joe DeRisi's laboratory). Provides hierarchical cluster analysis algorithms and graphical representation of data. (Eisen et al, PNAS, 95:14863-8, 2001)
4. Significance Analysis of Microarrays (SAM) and Prediction Analysis of Microarrays (PAM) (Robert Tibshirani and Gilbert Chu). SAM identifies array features with statistically significant differences in reactivity between sample groups. PAM performs sample classification from antibody reactivity data to provide a list of significant genes whose expression characterizes each sample group. (Tusher et al, PNAS, 98:5116-21, 2001; Tibshirani et al, PNAS, 99:6567-72, 2002)
General Approach
GenePix Pro 5.0 software (Axon Instruments) is used to extract the net median pixel intensities for individual features from the digital images produced by the GenePix 4000B scanner. Normalized median net digital fluorescence units (DFUs) are generated from the median values from 4-12 identical antigen features on each array. Significance Analysis of Microarrays (SAM) is applied to identify antigens with statistically-significant differences in array reactivity between and Predictive Analysis of Microarrays to identify antigens whose reactivity characterizes defined murine or human clinical sample groups. SAM results can be arranged into relationships using Cluster software. Results are displayed using TreeView software.
