Question: DeSeq2 MA plot
0
gravatar for niu.shengyong
23 months ago by
niu.shengyong30 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 • 2.0k views
ADD COMMENTlink written 23 months ago by niu.shengyong30
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 23 months ago • written 23 months ago by mastal5112.0k

I use DESeq2 1.14.1. Is it too old?

ADD REPLYlink written 23 months ago by niu.shengyong30

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 23 months ago by WouterDeCoster38k

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

ADD REPLYlink written 23 months ago by niu.shengyong30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1512 users visited in the last hour