Question: Do I have too many samples or are some samples causing issues?
gravatar for cmfield
15 days ago by
cmfield0 wrote:

I have RNASeq count data from 42 different conditions, 5 repeats per condition for a total of 210 samples, and approximately 37,000 genes. DESeq freezes up at the estimateDispersions step unless I slice the data down to ~50 samples or so. Is it the case that the calculation time scales up in the extreme, or is it something about one or more of my samples causing the freeze? I have tried parallelising the step with 120 cores, but to no avail, and I feel like it's perhaps a crash rather than just a long calculation because I can't cancel it (though that's often the case in R so who knows).

Any advice appreciated.

ADD COMMENTlink modified 15 days ago by Michael Love20k • written 15 days ago by cmfield0
gravatar for Michael Love
15 days ago by
Michael Love20k
United States
Michael Love20k wrote:

It's not "freezing", but just going slowly because the design matrix is very large (both number of samples and number of parameters). I'd recommend to use limma-voom.

ADD COMMENTlink written 15 days ago by Michael Love20k
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