Question: DESeq2:Why is there an oblique line in my MA picture, which happened before, what caused this?
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gravatar for xuyao15927402897
4 months ago by
xuyao159274028970 wrote:

My sample is RNA-Seq data from human Esophageal tissue, 9 control groups(normal), 2 experimental groups(Esophageal cancer),The result is Figure 1.Figure 1

I use featurecounts to count genes, this is my counts array

cancer deseq2 • 134 views
ADD COMMENTlink modified 4 months ago by Michael Love25k • written 4 months ago by xuyao159274028970
Answer: DESeq2:Why is there an oblique line in my MA picture, which happened before, wha
1
gravatar for Michael Love
4 months ago by
Michael Love25k
United States
Michael Love25k wrote:

Those lines are from genes with very low counts of genes, e.g. 2 counts in the treated group, 1 count in the control group. If you want to remove them you can perform some minimal filtering, e.g.:

keep <- rowSums(counts(dds) >= 10) >= x
dds <- dds[keep,]

Where you choose x to be a small number of samples.

ADD COMMENTlink written 4 months ago by Michael Love25k

Will removing these low counts have any bad effect, will I ignore the low-expression genes?

ADD REPLYlink modified 4 months ago • written 4 months ago by xuyao159274028970

It's pretty hard to achieve power for DE when there are say, only 2 samples with counts above 10. So setting x <- 3 will be fairly conservative in terms of FNR.

ADD REPLYlink written 4 months ago by Michael Love25k

Ok, thank you very much!

ADD REPLYlink written 4 months ago by xuyao159274028970
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