I need help on loading data to LIMMA I'm working with 44K Agilent microarrays. I'm novice in BioConductor, so I'm trying to follow instructions on the packages to deal with my data. I'm trying to load Feature Extraction raw data with > RG <- read.maimages(files = targets$fileName, path = loadPath, source = "agilent") and data seems to be loaded fine, where targets is experiment description file. It is loading all my 20 replicates, but when I checked RG data set with dim(RG) or show(RG) I realized that only 6195 rows have been loaded. It is the same situation independent on how many arrays I'm loading 1 or 28. Is there limit for number of spots in the package? I've tried to start as well with arrayMagic package and again didn't succeed to load even single array, After 10 min of loading I see error message stating that line 17000 has not proper amount of arguments. Thank you in advance for any suggestion -- Dr. Nataliya Yeremenko Universiteit van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands

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[BioC] Help on Loading AgilentData into LIMMANataliya, This is not due to the size of the file, but to special characters in the file itself causing premature end-of-file. Gordon replied, if I recall, that this was a bug in R 2.1.0 and has been fixed in R 2.2.0. Perhaps you could send version and sessionInfo, just to be sure what versions of everything you are using? Also, you might want to look in the archive for Gordon's specific answer. Sean ----- Original Message ----- From: Nataliya Yeremenko To: BioC Mailing List Sent: Monday, November 07, 2005 6:45 PM Subject: [BioC] Help on Loading AgilentData into LIMMA I'm coming back to my problem of import of Agilent data into the Bioconductor limma package. Version of R is 2.2.0 Limma as well is the newest possible as I've installed Bioconductor only two weeks ago. Each "target" file is Agilent 44K Human oligo microarray, produced by FeatureExtraction 7.5. I'm importing data into limma with: > RG <- read.maimages(files = targets$fileName, path = loadPath, source = "agilent") Afterwards checking the dimensions of RG with dim(RG) - 6195 rows only, with no difference how many target files I've been loading. I go further and checked the same function on another data set - Agilent custom 11K oligo microarrays extracted as well with Feature Extraction 7.5 (with the same default settings of Feature extraction procedure as for 44K). And to my surprise the target files have been loaded completely into LIMMA. Dim(RG) - 8635 rows. So the problem is that of 44K - maybe target files are to big? Does anybody have any suggestions? -- Dr. Nataliya Yeremenko Universiteit van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands tel. + 31 20 5257089 fax + 31 20 5257064 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

I'm coming back to my problem of import of Agilent data into the Bioconductor limma package. Version of R is 2.2.0 Limma as well is the newest possible as I've installed Bioconductor only two weeks ago. Each "target" file is Agilent 44K Human oligo microarray, produced by FeatureExtraction 7.5. I'm importing data into limma with: > RG <- read.maimages(files = targets$fileName, path = loadPath, source = "agilent") Afterwards checking the dimensions of RG with dim(RG) - 6195 rows only, with no difference how many target files I've been loading. I go further and checked the same function on another data set - Agilent custom 11K oligo microarrays extracted as well with Feature Extraction 7.5 (with the same default settings of Feature extraction procedure as for 44K). And to my surprise the target files have been loaded completely into LIMMA. Dim(RG) - 8635 rows. So the problem is that of 44K - maybe target files are to big? Does anybody have any suggestions? -- Dr. Nataliya Yeremenko Universiteit van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands tel. + 31 20 5257089 fax + 31 20 5257064