[BioC] ReadAffy gives Error

[James W. MacDonald]

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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>>
>>
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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