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Question: DeSeq2 MA plot
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gravatar for niu.shengyong
16 months ago by
niu.shengyong0 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 :https://drive.google.com/file/d/0ByJ9Aiypgye9aHNWSHlDZEk0dEk/view?usp=sharing

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)

 

 

 

ADD COMMENTlink modified 16 months ago by Michael Love19k • written 16 months ago by niu.shengyong0
1
gravatar for Michael Love
16 months ago by
Michael Love19k
United States
Michael Love19k wrote:

The visual artifacts are typically when one group (here control) is sequenced at much lower depth than the treated group in a two group comparison. The patterns are unavoidable. It is not great to have large differences in sequence depth across the conditions, but I don't have a decision boundary or anything at which it's too much of a problem. I would zoom out on the plot (e.g. to [-6,6]) so you can see which genes are being called DE if any.

ADD COMMENTlink written 16 months ago by Michael Love19k
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