R help - Sep 2007 - Error: cannot allocate vector of size...

Hi,

I want to change .RDA file to a text file. So I did as follows.
>load("my.rda")
>ls() ---> then it showed [1] exprs
>write.table(exprs,"C:\\my.txt",sep="\t")
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.

Thank you.
Jittima

Jittima Piriyapongsa <gtg894p at mail.gatech.edu> writes:
> Hi,
>
> I want to change .RDA file to a text file. So I did as follows.
>
>>load("my.rda")
>>ls() ---> then it showed [1] exprs
>>write.table(exprs,"C:\\my.txt",sep="\t")
>
> 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.

Martin
> Thank you.
> Jittima
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org