Question: DESeq2 analysis for low RNA input
0
gravatar for capricygcapricyg
11 weeks ago by
capricygcapricyg0 wrote:

Hello, there,

Our cells were treated in two tough conditions (A and B), and as a result, numbers of the survival cells were pretty low, particularly for condition A. The total mapped reads for condition A was about 10% of that for condition B. I wonder if I can still run DESeq2 for differential analysis between A and B.

Thanks a lot!

C.

deseq2 • 137 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by capricygcapricyg0

How about variance-mean dependence for low-reads sample? Does it still hold?

ADD REPLYlink written 11 weeks ago by capricygcapricyg0

Yes VST stills works if that is what you are asking?

ADD REPLYlink written 11 weeks ago by Michael Love25k
Answer: DESeq2 analysis for low RNA input
0
gravatar for Michael Love
11 weeks ago by
Michael Love25k
United States
Michael Love25k wrote:

What are the number of reads for the two groups (in millions)?

ADD COMMENTlink written 11 weeks ago by Michael Love25k

Condition B, we had 0.8-2 millions and condition A, only 0.04-0.15 million.

The numbers of the detected genes for condition B was about 5000 (human genome) and for A about 1500...

ADD REPLYlink written 11 weeks ago by capricygcapricyg0

I think this is a problem for any kind of DE analysis, because you can get a count of 20 in condition B, but a 0 in condition A under the null. We discuss this as a pathological case in the DESeq2 paper. One way to deal with this would be to filter out genes unless you see a positive count for all samples. This isn't ideal but otherwise you are subject to the problem that 0's which are compatible with the null will look like significant differences.

ADD REPLYlink written 11 weeks ago by Michael Love25k
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