[BioC] ReadAffy gives Error
boel.brynedal at ki.se
Wed Apr 4 22:15:57 CEST 2007
How much RAM is needed to read and analyze 88 hgu133plus2 arrays?
As I've understood it, the actual ReadAffy() part would not be a
problem, but the normalization. In this case I want to do all of the
quality controls, I want the AffyBatches.
I had the impression that 4GB would be enough.
On Wed, 2007-04-04 at 09:50 -0400, James W. MacDonald wrote:
> Boel Brynedal wrote:
> >>>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?
> Depends on what kind of chip you are using. It might work for older
> chips (e.g., hgu95av2), but probably not for the current generation of
> 3' arrays (e.g., hgu133plus2).
> > Is there a limitation for how much memory R can use? And, if there is,
> > how can I change this?
> There are limits on the size of objects, but you will not be hitting
> that here. On Linux R will take all the memory it requires without any
> intervention by you, so if you are getting this error you have hit the
> wall. Are you doing other memory-hungry things concurrently?
> There are ways around this that don't require purchasing RAM. First, you
> can use justRMA() which will undoubtedly be able to process all your
> chips. The downside is no AffyBatch, so you can't do QA plots of the raw
> Another alternative is to use read.probematrix(), which will read in
> just the PM and/or MM probes. You can use these data for quality
> assessment, etc, but you will be missing all the niceties that come with
> using an AffyBatch.
> >>>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).
> You should use biocLite() for all package installation. If you just grab
> things and install directly you always run the risk that you are
> installing something that is an incorrect version for the version of
> R/BioC that you have. Using biocLite() ensures that you get the correct
> For instance, simpleaffy 2.4.2 is not the correct version for use with
> BioC 1.9. You should have 2.8.0. This doesn't explain the isVersioned
> error, as your affy/Biobase/affyio are all correct versions. It is
> probably just because you ran out of memory.
> > This is my 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:
> >  "grid" "splines" "tools" "stats" "graphics"
> > "grDevices"
> >  "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
> >>>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.
> >>>Bioconductor mailing list
> >>>Bioconductor at stat.math.ethz.ch
> >>>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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