DeSeq2 MA plot

Question

[niu.shengyong]

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)

[mastal511]

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

[niu.shengyong]

I use DESeq2 1.14.1. Is it too old?

[WouterDeCoster]

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.

[niu.shengyong]

Thanks for your notice. Sorry I'm quite new in this area. I'll avoid this next time. Thanks again!