[BioC] ReadAffy gives Error

[Boel Brynedal]

Hi again,
Thanks for the answer Jim, please se my response below. 
On Tue, 2007-04-03 at 11:15 -0400, James W. MacDonald wrote:
> Hi Boel,
> 
> Boel Brynedal wrote:
> > Dear all!
> > 
> > I have 88 CEL files, and I'm about to do some initial quality control.
> > Right now I just want to read in the raw data. I have a 64 bit Linux
> > RedHat with 4GB ram. I have set the wd to the same directory as my
> > files, and the following happens:
> > 
> >>rData<-ReadAffy()
> > 
> > Error: cannot allocate vector of size 931491 Kb
> 
> This error indicates that you need more RAM.

But I have 4GB of RAM, shouldn't that be enough? 
Is there a limitation for how much memory R can use? And, if there is,
how can I change this?

> 
> > Error in isVersioned(object) : error in evaluating the argument 'object'
> > in selecting a method for function 'isVersioned'
> 
> Not sure about this one. It may just be an artifact of the first error, 
> or indicate a mismatch in your package versions. How did you install the 
> BioC packages? What is your sessionInfo()?

Bioconductor was installed using biocLite(), other packages where also
downloaded and installed (using i.e. R CMD INSTALL simpleaffy).

This is my sessionInfo()
> sessionInfo()
R version 2.4.1 (2006-12-18)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
 [1] "grid"      "splines"   "tools"     "stats"     "graphics"
"grDevices"
 [7] "utils"     "datasets"  "methods"   "base"

other attached packages:
 simpleaffy  genefilter    survival     IDPmisc     lattice     affyPLM
    "2.4.2"    "1.12.0"      "2.30"     "0.9.1"   "0.14-16"    "1.10.0"
      gcrma matchprobes    affydata        affy      affyio     Biobase
    "2.6.0"     "1.6.0"    "1.10.0"    "1.12.2"     "1.2.0"    "1.12.2"

I can read 4 CEL files without any problems, so maybe this is a memory
problem all together, but I really thought 4 GB of RAM would be enough.

Thankful for any advice,
Boel
> 
> Best,
> 
> Jim

> > Any suggestions to what is wrong? 
> > As you might imagine, I am quite new in this field. 
> > 
> > Best regards,
> > Boel Brynedal, PhD student, Karolinska Institutet, Sweden.
> > 
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> 
>