gcrma error " 'Calloc' could not allocate memory"
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@giuseppe0525-14327
Last seen 3.1 years ago

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)
cels

celfiles.gcrma <- gcrma(celfiles)
celfiles.gcrma

"

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!

 

gcrma error • 1.6k views
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@james-w-macdonald-5106
Last seen 43 minutes ago
United States

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.
 

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Thank you very much! I'll try it.

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