Question

edgeR rrbs estimateDisp runs forever and doesn't seem to finish

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Archana • 0

@archana-24034

Last seen 3.5 years 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

edgeR • 562 views

ADD COMMENT • link updated 3.5 years ago by Gordon Smyth 50k • written 3.5 years ago by Archana • 0

score 0 · Answer 1 · 2020-10-30

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Gordon Smyth 50k

@gordon-smyth

Last seen 5 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

ADD COMMENT • link 3.5 years ago Gordon Smyth 50k