I am using DESeq2 to perform some differential expression analysis between 3 levels of a disease condition. However, I am getting a strange looking MA-plot when i compare some of the conditions. I am trying to understand what could be the reason for the skewness in my MA-plot.
Any help will be greatly appreciated.
I have provided the PCA plot of the different samples as well as one of the MA-plots (comparing LTNP vs VC). The analysis steps I have taken are below:
sampleFiles <- grep("count",list.files(directory),value=TRUE) sampleCondition<-c(rep("EC", 3), rep("LTNP", 4), rep("VC",4)) sampleTable<-data.frame(sampleName=sampleFiles, fileName=sampleFiles, condition=sampleCondition) ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design=~condition) dds <- ddsHTSeq[ rowSums(counts(ddsHTSeq)) > 1, ] rld <- rlog(dds, blind = FALSE) dds <- DESeq(ddsHTSeq2) res <- results(dds, contrast=c("condition", "LTNP", "VC"))