[R] Error: cannot allocate vector of size...
mtmorgan at fhcrc.org
Tue Sep 25 00:47:27 CEST 2007
Jittima Piriyapongsa <gtg894p at mail.gatech.edu> writes:
> I want to change .RDA file to a text file. So I did as follows.
>>ls() ---> then it showed  exprs
> I was successful with the first .RDA file. Then I used the same
> commands with another .RDA file (172 MB)which is 4 times bigger than
> the first file (41.2 MB). When I put the last command
> (write.table), it showed as below.
> Error: cannot allocate vector of size 92.8 Mb
> In addition: Warning messages:
> 1: The exprSet class is deprecated, use ExpressionSet instead
> 2: The exprSet class is deprecated, use ExpressionSet instead
> 3: The exprSet class is deprecated, use ExpressionSet instead
> 4: The exprSet class is deprecated, use ExpressionSet instead
> What could be a problem in this case? Is it the memory problem? I
> believe I have enough RAM and disk space in my computer.
R has run out of RAM to allocate memory -- it has already allocated
memory, and now cannot allocate an addition 92.8 MB.
Is write.table doing what you want? A different approach would be to
write two tables, one with the 'expression' data
> write.table(exprs(exprs), "C:\\myExprs.txt", sep="\t")
the other with the description of phenotypes
> write.table(pData(exprs), "C:\\myPheno.txt", sep="\t")
This might be more memory efficient, but might also get your data in a
more immediately useable format.
> Thank you.
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Bioconductor / Computational Biology
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