Item Type: Appointment Begin time: Mon, 02 Oct 2006 05:00 pm +0000 Duration: 1 Hour Location: Hi, I've a problem using limma with quantarray output files. I've changed all output files to ANSI format, because the original Unicode format is not accepted by limma. I'm able to use one file per time without any trouble but when I try to load more than one file using a "target" file using, >target<-readTargets(file="targets.txt",path="C:\\Playground\\CrossTes t") >RG<-read.maimages(target,source="quantarray",path="C:\\Playground\\Cr ossTest") I receive an error message like: Read C:\Playground\CrossTest/PA52-Export.txt Error in if (skip > 0) readLines(file, skip) : argument is of length zero How can I solve this problem? Kind Regards Alessio

> Hi, > > I've a problem using limma with quantarray output files. I've changed all output files to ANSI format, > because the original Unicode format is not accepted by limma. > I'm able to use one file per time without any trouble but when I try to load more than > one file using a "target" file using, > > >target<-readTargets(file="targets.txt",path="C:\\Playground\\CrossTes t" ) > > >RG<-read.maimages(target,source="quantarray",path="C:\\Playground\\Cr os sTest") > > I receive an error message like: > > Read C:\Playground\CrossTest/PA52-Export.txt > Error in if (skip > 0) readLines(file, skip) : > argument is of length zero > > How can I solve this problem? > > Kind Regards > > Alessio > Alessio, I had a similar problem in a recent version of limma (not sure which version you're using). If you edit the source for read.maimages, and look for the second instance of the line: skip <- grep("Begin Data", firstfield) and comment this out. Save this as your own function, and it should work okay. This will only work if all your quantarray files have the data (as flagged by the "Begin Data" string) starting at the same line. If this is not the case, then you'll need to find the instance of the phrase "nlines=100" just above the skip assignment, and remove it/customise it to your files (and uncomment the skip assignment) Hope this helps - Gavin -- Gavin Kelly (DPhil) Senior Statistician Bioinformatics & Biostatistics, Room 708 Cancer Research UK 44 Lincoln's Inn Fields London WC2A 3PX United Kingdom

Dear Gordon and Gavin, many thanks for your prompt answer and support! Cheers Alessio -----Original Message----- From: "Gordon K Smyth" <smyth@wehi.edu.au> To: "Gavin Kelly" <gavin.kelly at="" cancer.org.uk="">, "Alessio Venier" <0509388V at student.gla.ac.uk> Date: Wed, 4 Oct 2006 21:56:03 +1000 (EST) Subject: [BioC] Limma and Quantarray files Dear Alessio and Gavin, Thanks for pointing out the problem with reading quantarray files. The bug has now been fixed in limma 2.9.1. limma now reads the annotation columns for quantarray files as well. Best wishes Gordon > Date: Wed, 4 Oct 2006 09:43:50 +0100 > From: "Gavin Kelly" <gavin.kelly at="" cancer.org.uk=""> > Subject: Re: [BioC] Limma and Quantarray files > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: > <1BFC6DAE48E6D4478BDFF41C012CD311FC4FB4 at uk-lif- lexc02.crwin.crnet.org> > Content-Type: text/plain; charset="us-ascii" > >> Hi, >> >> I've a problem using limma with quantarray output files. I've changed > all output files to ANSI format, >> because the original Unicode format is not accepted by limma. >> I'm able to use one file per time without any trouble but when I try > to load more than >> one file using a "target" file using, >> >> >>target<-readTargets(file="targets.txt",path="C:\\Playground\\CrossTe st" > ) >> >> >>RG<-read.maimages(target,source="quantarray",path="C:\\Playground\\C ros > sTest") >> >> I receive an error message like: >> >> Read C:\Playground\CrossTest/PA52-Export.txt >> Error in if (skip > 0) readLines(file, skip) : >> argument is of length zero >> >> How can I solve this problem? >> >> Kind Regards >> >> Alessio >> > > Alessio, > I had a similar problem in a recent version of limma (not sure which > version you're using). If you edit the source for read.maimages, and > look for the second instance of the line: > > skip <- grep("Begin Data", firstfield) > > and comment this out. Save this as your own function, and it should > work okay. This will only work if all your quantarray files have the > data (as flagged by the "Begin Data" string) starting at the same line. > If this is not the case, then you'll need to find the instance of the > phrase "nlines=100" just above the skip assignment, and remove > it/customise it to your files (and uncomment the skip assignment) > > Hope this helps - Gavin > > -- > Gavin Kelly (DPhil) Senior Statistician > Bioinformatics & Biostatistics, Room 708 > Cancer Research UK > 44 Lincoln's Inn Fields > London WC2A 3PX > United Kingdom ure which > version you're using). If you edit the source for read.maimages, and > look for the second instance of the line: > > skip <- grep("Begin Data", firstfield) > > and comment this out. Save this as your own function, and it should > work okay. This will only work if all your quantarray files have the > data (as flagged by the "Begin Data" string) starting at the same line. > If this is not the case, then you'll need to find the instance of the > phrase "nlines=100" just above the skip assignment, and remove > it/customise it to your files (and uncomment the skip ass