I am running DESeq2 to perform a differential expression analysis two treatment conditions (Treat vs. Control) of a wasp infection in a beetle species. However I got some strange looking MA-plot when comparing some conditions.
There is an obvious set of outlier red dots in the down-regulated region that looks very strange. Can anybody explain what causes such results?
The count data was imported from Salmon output. The R command I used are below:
filesevipus12h<- c("quant1.sf", "quant2.sf", "quant3.sf", "quant4.sf", "quant5.sf", "quant6.sf") names(filesevipus12h) <- c("Treat_12h_rep1", "Treat_12h_rep2", "Treat_12h_rep3", "Control_12h_rep1", "Control_12h_rep2", "Control_12h_rep3") txifilesevipus12h <- tximport(filesevipus12h, type="salmon", tx2gene=tx2genepus)
ddsTCpus12 <- DESeqDataSetFromTximport(txifilesevipus12h, colData=colDatapus12, design=~ Treatment) ddsTCpus12 <- DESeq(ddsTCpus12)
pus12res <- results(ddsTCpus12, alpha=0.05) plotMA(pus12res, main=paste0('G. pusilla'), ylim=c(-8,8))
Any help will be greatly appreciated. Thanks
I am having problem inserting images in biostar, the direct link to the DEseq2 image is below: