DeSeq2 MA plot
I use the following codes and generate this MA plot. It looks quite weird for me. Is there any problem I should take care of? Thanks! MA plot
ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory = directory,
design=~condition)
#ddsHTSeq
colData(ddsHTSeq)$condition<-factor(colData(ddsHTSeq)$condition, levels=c('control','test'))
dds<-DESeq(ddsHTSeq)
res<-results(dds)
res<-res[order(res$padj),]
head(res)
plotMA(dds, ylim=c(-2,2), main='M', alpha=0.1)
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What version of DESeq 2 are you using? Note that the MA plots shown in the current DESeq2 vignette plot res or resLFC, and you are plotting dds.
Link to DESeq2 vignette:
https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
I use DESeq2 1.14.1. Is it too old?
Hello niu.shengyong!
It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/96645/
This is typically not recommended as it runs the risk of annoying people in both communities.
Thanks for your notice. Sorry I'm quite new in this area. I'll avoid this next time. Thanks again!