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.

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor