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

[Saif Ur-Rehman [guest]]

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

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