Deferential Gene Expression is not generating meaningful p-values for rawp and adbj

[Sathish Periyasamy]

Hi,

I am using Affymetrix exon arrays to generate differential gene expression values for tumor - normal pairs. However I am not using replicates and results show rawp and adbj as 1. Please advise me whether I could use the fold change values without inferring to the p-values in the output file.

Sathish

[Nathan Salomonis]

Hi Sathish,

The default is to only use the fold change for filtering the differential gene expression values when replicates are not present. The default fold cutoff is 2, but you can change this by selecting the option "run immediately" for GO-Elite (last option in the expression analysis parameters window). The files this cutoff will effect are the GO-Elite input files, the input for PCA and hierarchical clustering analysis. The same is true for alternative exon analyses, where only the fold change cutoff is used (separate splicing-index fold change parameter in the alternative splicing parameter menu).

Best,
Nathan

Sathish

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