Hi, My name is Candida Vaz, a post doctoral research fellow at the Bioinformatics Institute (BII) Singapore.
I am using edgeR package for my RNASeq data analysis. The User guide is extremely helpful, and I have been following it well. However, I am not able to find the R command to obtain the list of Differentially expressed genes at a Fold change (log-fold change) and FDR cut-off. The R command summary:
summary(de <- decideTestsDGE(et, p=0.05, adjust="BH"))
only gives the summary/number of DE genes. And the command topTags:
topTags(et, n=10, adjust.method="BH", sort.by="PValue")
gives the information/list of the top "n" number of DE genes.
I am interested in getting the full list of DE genes at the log fold change cut-off of (+-1) and FDR cut-off of <0.05. Would appreciate your help with this query.
Thanks a lot.