edgeR rrbs estimateDisp runs forever and doesn't seem to finish
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Archana • 0
@archana-24034
Last seen 4 months ago

Hi , I'm trying to perform rrbs dme analysis using edgeR on 50 samples (5 replicates per timepoint /sex). It seems to be running forever (>8 hours) and not produce any output. Design matrix has 50 samples , 10 conditions. Is there anyway I can speed up the dispersion estimation?


y <- estimateDisp(y, design, trend="none",subset=5000)

Thanks, Archana

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@gordon-smyth
Last seen 2 hours ago
WEHI, Melbourne, Australia

I wonder how many rows of data you have, as estimateDisp doesn't take that long for me with 50 samples. Anyway, see my answer to a previous question for a faster workaround:

scalability of edgeR on RRBS methylation data

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