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Published 20 hours ago • verified publisher icon gagneurlab

Predefined covariates

Open gk1610 opened this issue 2 years ago • 0 comments

I am working on epigenomic data to find outliers. I have over ~350K features. I requested for 15 cores but I keep getting the following error. Can I just use PEER covariate subtracted matrix? At what step I can implement that? or you have other suggestions to improve the implementation?

ncores <- 15 register(MulticoreParam(ncores, ncores*2, progressbar = TRUE)) ods <- OutriderDataSet(countData=rawReads_cpm) ods <- estimateSizeFactors(ods) ods <- findEncodingDim(ods, BPPARAM=bpparam(), params = seq(2,50,by=2)

| | 0%Error in mcfork(detached) : unable to fork, possible reason: Cannot allocate memory In addition: Warning message: In parallel::mccollect(wait = TRUE) : 18 parallel jobs did not deliver results

gk1610 avatar May 19 '22 22:05 gk1610