Question: gcrma error " 'Calloc' could not allocate memory"
gravatar for giuseppe0525
13 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 13 months ago by James W. MacDonald48k • written 13 months ago by giuseppe05250
gravatar for James W. MacDonald
13 months ago by
United States
James W. MacDonald48k 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 13 months ago by James W. MacDonald48k

Thank you very much! I'll try it.

ADD REPLYlink written 13 months ago by giuseppe05250
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