Question: DESeq: large difference in number of replicates per condition
gravatar for krc3004
12 months ago by
krc300410 wrote:

Hi all,

I have a general question about the model estimation used by DESeq.  There have been many posts on whether or not DESeq works well with a small number/no replicates, but I'm wondering if it's appropriate to use DESeq for differential analysis across two conditions, where one condition has a small number of replicates (say, 5) and the other has a huge number (in the 100s).  The particular phenotype that we are looking at in our (clinical) data is quite rare, but we'd still like to test for differential expression.  Usually I would provide a reproducible example but these data are sensitive...

In this case, does it make sense to use DESeq?  Would it make sense to, say, randomly sample some of the replicates from the condition with 100s of replicates and run multiple tests?  I'm reading the original DESeq2 paper to try to understand how the model is built but any tips would be much appreciated.  Thank you!

ADD COMMENTlink modified 12 months ago by Michael Love19k • written 12 months ago by krc300410
gravatar for Michael Love
12 months ago by
Michael Love19k
United States
Michael Love19k wrote:

You shouldn't downsample the condition with 100s of replicates. There is nothing special to do, but you should note that the dispersion estimate will be mostly influenced from the group with more replicates. You can look at plotCounts afterward to verify that the top genes make sense, and are not affected by any artifact.

ADD COMMENTlink written 12 months ago by Michael Love19k

Michael, thanks very much for your help!  I will proceed without downsampling.

ADD REPLYlink written 12 months ago by krc300410

I would add that you should also pay attention to outlier filtering/replacement (see DESeq minReplicatesForReplace) if you expect your large group to be heterogenous. I've seen people run into trouble with that when handling large groups.

ADD REPLYlink modified 12 months ago • written 12 months ago by igor20
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