Question: gcrma error " 'Calloc' could not allocate memory"
gravatar for giuseppe0525
3 months ago by
giuseppe05250 wrote:

hello, everyone!

can anyone help solve the problem I came across when using 'gcrma'?

the code was shown as followed:


untar("GSE32529_RAW.tar", exdir="data")
cels <- list.files("data/", pattern = "[gz]")
sapply(paste("data", cels, sep="/"), gunzip)

celfiles.gcrma <- gcrma(celfiles)


The return was


Adjusting for non-specific binding.......................

Error in rowSums((x.evaluate <= rep(ranges[2L, ], rep_len(M, D))) & (x.evaluate >=  : 
  'Calloc' could not allocate memory (496468 of 16 bytes)


Is it because of the lack of memory of my PC? And how can I fix it?

thank you!


ADD COMMENTlink modified 3 months ago by James W. MacDonald45k • written 3 months ago by giuseppe05250
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald45k wrote:

You could try justGCRMA, which is supposed to be a bit less memory intensive. But 224 arrays is a lot if you don't have a reasonable amount of RAM. The obvious other alternatives are to get more RAM, or to use a large-ish EC2 instance and the Bioconductor AMI.

ADD COMMENTlink written 3 months ago by James W. MacDonald45k

Thank you very much! I'll try it.

ADD REPLYlink written 3 months ago by giuseppe05250
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