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Hi Sikha, posting the command that caused the error and also the error message would be helpful. In addition the output of sessionInfo() could help to identify problems with potentially outdated versions of your R packages. afaik Agi4x44PreProcess calls the read.maimages function of the limma package to read the files. could you test if read.maimages(filename, source="agilent) works for you? best Tobias On Aug 19, 2009, at 6:09 AM, shikha sinha wrote: > Hi, > > I am using Agi4x44PreProcess for preprocessing my agilent microarray > data. I have extracted data using Feature Extraction v10.5. So, > Agi4x44PreProcess is unable to read my raw data, But in Help Pdf it > has been written there that we can use it for FE 9.5 and later on > versions of FE. > > Please Help me > > Thanks, > Sikha > > > > See the Web's breaking stories, chosen by people like you. > Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ---------------------------------------------------------------------- Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, M?nchen D

hi sikha apparently read.AgilentFE has to read information that is only written in a FULL feature table format export (which comprises e.g. chr_coord and sequence) in FE 10.5. most likely you did only COMPACT output (the default). did you check the FULL option when doing the extraction? best tobias On Aug 19, 2009, at 10:15 AM, shikha sinha wrote: > Hi, > > Yes, I can use readmaimages in limma but I feel using > Agi4x44PreProcess will make my work easier. I have used read.targets > for reading my target file and then read.AgilentFE for reading my > text raw data files. Please find below the commands I used and error > message I got: > > > targets=read.targets(infile="targets.txt") > > Target File > FileName > treatment GErep > US83000164_251485040272_S01_GE1_105_Dec08_1_1 > US83000164_251485040272_S01_GE1_105_Dec08_1_1.txt a 1 > US83000164_251485040272_S01_GE1_105_Dec08_1_2 > US83000164_251485040272_S01_GE1_105_Dec08_1_2.txt b 2 > > > dd=read.AgilentFE(targets,makePLOT=FALSE) > Read US83000164_251485040272_S01_GE1_105_Dec08_1_1.txt > Read US83000164_251485040272_S01_GE1_105_Dec08_1_2.txt > INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord > SCANN THE DATA USING AFE 9.5.3.1 > Error in read.AgilentFE(targets, makePLOT = FALSE) : > the script will stop now > > Thanks & Regards > Sikha > > --- On Wed, 19/8/09, Tobias Straub <tstraub at="" med.uni-muenchen.de=""> > wrote: > > From: Tobias Straub <tstraub at="" med.uni-muenchen.de=""> > Subject: Re: [BioC] Regarding Agi4x44PreProcess > To: "shikha sinha" <shikhakk2002 at="" yahoo.co.in=""> > Cc: bioconductor at stat.math.ethz.ch > Date: Wednesday, 19 August, 2009, 12:38 PM > > Hi Sikha, > > posting the command that caused the error and also the error message > would be helpful. In addition the output of sessionInfo() could help > to identify problems with potentially outdated versions of your R > packages. > > afaik Agi4x44PreProcess calls the read.maimages function of the > limma package to read the files. could you test if > read.maimages(filename, source="agilent) works for you? > > best > Tobias > > On Aug 19, 2009, at 6:09 AM, shikha sinha wrote: > > > Hi, > > > > I am using Agi4x44PreProcess for preprocessing my agilent > microarray data. I have extracted data using Feature Extraction > v10.5. So, Agi4x44PreProcess is unable to read my raw data, But in > Help Pdf it has been written there that we can use it for FE 9.5 and > later on versions of FE. > > > > Please Help me > > > > Thanks, > > Sikha > > > > > > > > See the Web's breaking stories, chosen by people like you. > Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives:http://news.gmane.org/gmane.science.biology.in formatics.conductor > > ---------------------------------------------------------------------- > Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, M?nchen D > > > > > > Looking for local information? Find it on Yahoo! Local ---------------------------------------------------------------------- Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, M?nchen D