RNA-seq differentially expressed gene finding methods
Son Pham <spham-xrR1t/[email protected]> Fri, 5 Sep 2014 09:44:01 -0700
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <CAKUmEKErQpMVyvr-ig0Ug3iVJLT8+ajFuku2MgPkYRWvd8NLkA@mail.gmail.com> |
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) Thanks, Son. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor