error in gcrma function
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@farahqureshi5-12184
Last seen 4.1 years ago

Greetings!!

can anyone help me with this error encountered and how it can be rectified. is it due to less memory in my system or any other issue

celfiles.gcrma = gcrma(celfiles)
Adjusting for optical effect..
Error: cannot allocate vector of size 124.0 Mb

thanking in anticipation

gcrma • 556 views
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Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …

This is indeed a typical error of having all available RAM exhausted.

Two suggestions:

- perform RMA normalization (instead of gcRMA) [celfiles.rma <- rma(celfiles)]; AFAIK RMA requires less memory.

- if applicable, be sure to run the 64bits version of R. On 64 bit operating systems more memory can be used than on 32 bit OS, thus if possible take advantage of it.

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Another alternative is to use justGCRMA, which is intended to be less memory intensive.

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