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Two chip Analysis (3' Ivt probe level)

The Two Chip Analysis (Probe Level) allows the user to generate p-values and estimates for two-chip comparisons. It uses probe level data in order to generate these comparisons. Note: the pvalues are calculated based on the assumption that all the probes in the same probe set are independent (and this is usually not true). If more than two chips are specified, it will generate pairwise comparisons for every combination (up to 10 chips at one time are allowed).

This is not a recommended method for analysis, but can be used in cases where the user does not have any biological replicates. This command opens the Two Chip Analysis window:




  • The window allows the user to specify CEL files using the Add, Add Folder, and Add List buttons.


  • For options, the user is shown the Chip Type (3'IVT, Gene or exon array). For exon arrays, the user can specify an analysis mode (gene_core, exon_core, gene_extended, etc..).
  • Two analysis types are provided, Wilcoxon test ( or T-test.


Clicking Submit will generate a new Table in the Solution Explorer. This Table includes the estimates and pvalues for each of the pairwise comparisons.