[BioC] Aroma query (Follow up to thread: \"Reading 5000 celfiles with ReadAffy\" )

[Henrik Bengtsson]

FYI,

this query is handled via the aroma mailing list, cf.
http://aroma-project.org/forum/topic/AM4zdO1Fi60

/Henrik

On Tue, Feb 28, 2012 at 3:54 AM, Saif Ur-Rehman [guest]
<guest at bioconductor.org> wrote:
>
> Hi guys,
>
> Thanks a lot for all your help.
>
> We tried using the aroma library to normalise the 5000+ celfiles and it seemed to run fine.
>
> However it stopped reading in Celfiles after 2,246 files after about 11 hours. It appears to fail silently.
>
> The code used was as follows:
>
> setwd("path")
> library(aroma.affymetrix)
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> chipType <- "HG-U133A"
> cdf <- AffymetrixCdfFile$byChipType(chipType)
> print(cdf)
> cs <- AffymetrixCelSet$byName("CELFILES", cdf=cdf)
> print(cs)
> bc <- RmaBackgroundCorrection(cs)
> csBC <- process(bc,verbose=verbose)
>
>
> The code appears to conclude but on inspection it only placed 2,246 in the output probeData folder.
>
> I was wondering if anyone has encountered a similar issue.
>
> Thanks in advance.
>
> Saif Ur-Rehman
>
>
>
>
>  -- output of sessionInfo():
>
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] Biobase_2.12.2         aroma.affymetrix_2.4.0 affxparser_1.24.0      aroma.apd_0.2.0
>  [5] R.huge_0.3.0           aroma.core_2.4.6       aroma.light_1.22.0     matrixStats_0.4.3
>  [9] R.rsp_0.7.1            R.cache_0.6.1          R.filesets_1.1.4       digest_0.5.1
> [13] R.utils_1.11.0         R.oo_1.8.3             affy_1.30.0            R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.20.0         preprocessCore_1.14.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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