Hi, For an RNA-seq data, I have found the significant DE genes based on FDR < 0.05 using the exactTest() function. Now I need to rank these DE genes based on the expression level (count values). What is the correct way of doing it? Thank you in advance.

If I'm not mistaken, running topTags on the result from the exactTest function will give you a table of DE genes, and this table will include a "logCPM" column that represents the mean log expression of the gene. You can simply sort the table by this column. On 12/12/2012 05:22 AM, Fatemehsadat Seyednasrollah wrote: > Hi, > > For an RNA-seq data, I have found the significant DE genes based on FDR < 0.05 using the exactTest() function. > Now I need to rank these DE genes based on the expression level (count values). What is the correct way of doing it? > > Thank you in advance. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor