R error allocMatrix

Question

Hi all,

I tried to download a certain number of Affiletrix CEL files with the standard BioConductor command (R 2.8.1 on 64-bit Linux, 72 GB RAM)

abatch<-ReadAffy()

But I keep getting this message:

Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  : 
  allocMatrix: too many elements specified

What is the general meaning of this allocMatrix error? Is there a way to increase the maximum size?

thanks

Answer 1

The problem is that all the main functions use INT instead of LONG to generate R objects. For example, your error message comes from array.c in / src / main

if ((double)nr * (double)nc > INT_MAX)
    error(_("too many elements specified"));

where nr and nc are the integers generated earlier for the number of rows and columns of your matrix:

nr = asInteger(snr);
nc = asInteger(snc);

, , LONG, , array.c, , . , , , . , R 3.x , , , ...

Answer 2

afymetrix, aroma.affymetrix.

, - () , , , R, - "" ( BioC). , , R 2.10, .

Answer 3

. , aroma. * allocMatrix() int longs, , - . . , .

/ ( . *)