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I am beginning my PhD in transcriptome (affymetrix assay) analysis.

I have an expression matrix (trans_data : 32000 genes x 620 samples), and a clinical matrix (clin_data : 620 samples x 42 clinical caracteristics). The samples belong to 1 of the 4 populations A-B-C-D. I'd like to draw comparision of gene expression between population A and B without triying to bind the two matrix.

I'd like to optain a matrix with mean expression of each genes in the two population, then pvalue, then adjusted p value.

Then I could select only differentially expressed genes (padj < 0,05).

thanks for your help. Alain

Alain_LU
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Can't answer your question directly without a clear reproducible example but you might want to check out the rather excellent tableone package

B_Real
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