Question: DeSeq2 MA plot
0
gravatar for niu.shengyong
2.2 years ago by
niu.shengyong40 wrote:

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)
rna-seq deseq2 maplot • 2.3k views
ADD COMMENTlink written 2.2 years ago by niu.shengyong40
1

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by mastal5112.0k

I use DESeq2 1.14.1. Is it too old?

ADD REPLYlink written 2.2 years ago by niu.shengyong40

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.

ADD REPLYlink written 2.2 years ago by WouterDeCoster40k

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

ADD REPLYlink written 2.2 years ago by niu.shengyong40
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