[BioC] ReadAffy gives Error

[Boel Brynedal]

Dear all,

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.

Best,
Boel

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 
> data.
> 
> 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 
> thing.
> 
> 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.
> 
> Best,
> 
> Jim
> 
> 
> 
> 
> > 
> > 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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> >>
> >>
> > 
> 
>