[BioC] RNA-seq differentially expressed gene finding methods

Son Pham spham at salk.edu
Fri Sep 5 18:44:01 CEST 2014

Dear all,
I know that we have quite very good packages (edgeR, deseq) that calculate
the list of differentially expressed genes in 2 conditions (with
replicates) from raw counts. But I do not know what is wrong with the
following simple approach (and whether other people have been using it):

1. Get the (estimated) tpm/fpkm for each gene in each sample
2. Do a t-test for two groups on each gene.
3. Adjust the p value for multiple tests (p-adj)



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