If you give the full path as part of the filenames to justRMA then set celfile.path="" Best, Ben On Tue, 2006-08-22 at 07:22 -0700, D.Enrique ESCOBAR ESPINOZA wrote: > may i haven t explained the things correctly > may be because my mother tongue is spanish & my second one is > french... > you had a good idea, but the cel files i want can be in diferent > directories, > maybe i want to normalize (nrom) 10 hgu133a celfiles that are in 10 > different paths or directories... > > Thanks > --- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > > > Please don't reply just to me. The idea of a list is to keep the > > questions and answers available for others as well. > > > > I don't understand your response. How does this duplicate data? > > Also, > > what is your 'norm'? > > > > My understanding of your original question was that you wanted to > > operate on celfiles that are not in your working directory, which > > is > > what the celfile.path argument is for. Am I missing something? > > > > Best, > > > > Jim > > > > D.Enrique ESCOBAR ESPINOZA wrote: > > > i don t want to duplicate data, > > > my norm should be in another place than my cel files > > > > > > --- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > > > > > > > > >>Hi Enrique, > > >> > > >>There is probably a way to use a file like that, but wouldn't it > > be > > >> > > >>easier to just pass the path to your call to justRMA()? > > >> > > >>eset <- justRMA(celfile.path = > > "/atlas/affy/proto_GQ/GQ005/M/20/") > > >> > > >>Best, > > >> > > >>Jim > > >> > > >> > > >>D.Enrique ESCOBAR ESPINOZA wrote: > > >> > > >>>i have decided to read cel files from a list containing full > > path > > >> > > >>to > > >> > > >>>each cel files, > > >>>one per line: > > >>>&$>head /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/CEL.list > > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL > > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL > > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL > > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL > > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL > > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL > > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL > > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL > > >>>in R console i ve done: > > >>> > > >>> > > >>>>(cels =celslist ); > > >>> > > >>>[[1]] > > >>>[1] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL" > > >> > > >>>[2] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL" > > >> > > >>>[3] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL" > > >> > > >>>[4] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL" > > >> > > >>>[5] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" > > >> > > >>>[6] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL" > > >> > > >>>[7] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" > > >> > > >>>[8] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" > > >> > > >>> > > >>>>(cels1=celslist[[1]]); > > >>> > > >>>[1] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL" > > >> > > >>>[2] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL" > > >> > > >>>[3] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL" > > >> > > >>>[4] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL" > > >> > > >>>[5] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" > > >> > > >>>[6] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL" > > >> > > >>>[7] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" > > >> > > >>>[8] > > >> > > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" > > >> > > >>>in the fisrt caSE <(cels =celslist)> i have this error: > > >>>Error in just.rma(filenames = l$filenames, phenoData = > > >> > > >>l$phenoData, > > >> > > >>>description = l$description, : > > >>> Could not open file > > >>> > > >> > > > > > > /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/c("/atlas/affy/proto_GQ/GQ 005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL", > > > > > > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL", > > > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL", > > > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL", > > > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL", > > > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL", > > > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL", > > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" > > >>>in the last case <(cels1=celslist[[1]])> i ve this error: > > >>>Error in just.rma(filenames = l$filenames, phenoData = > > >> > > >>l$phenoData, > > >> > > >>>description = l$description, : > > >>> Could not open file > > >>> > > >> > > > > > > /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2//atlas/affy/proto_GQ/GQ005 /M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL > > > > > >>>can someone tell me how to edit my CEL.list file in order to put > > >> > > >>1 > > >> > > >>>absolute path to each *.CEL and force R to normalize in the > > >> > > >>current > > >> > > >>>directory *.CEL that are in other directories? > > >>> > > >>>_______________________________________________ > > >>>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 > > >> > > >> > > >>-- > > >>James W. MacDonald, M.S. > > >>Biostatistician > > >>Affymetrix and cDNA Microarray Core > > >>University of Michigan Cancer Center > > >>1500 E. Medical Center Drive > > >>7410 CCGC > > >>Ann Arbor MI 48109 > > >>734-647-5623 > > >> > > >> > > >>********************************************************** > > >>Electronic Mail is not secure, may not be read every day, and > > >>should not be used for urgent or sensitive issues. > > >> > > > > > > > > > > > > -------------------------------------------------- > > > D.Enrique ESCOBAR ESPINOZA > > > (DESS Bioinfomatique > > > B.Sc. Biologie Moleculaire > > > === message truncated === > > _______________________________________________ > 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

You can specify several paths as such: cel.locations<-c("/directory1","/directory2") rma.Eset<-justRMA(celfile.path=cel.locations) Which saves you the trouble of itemizing the locations of particular cel files. Regards, Duane Hassane _________________________________________________ Duane C. Hassane, Ph.D. Center for Pediatric Biomedical Research University of Rochester Medical Center NOTICE OF CONFIDENTIALITY This message contains information which may be confidential and privileged. Unless you are the addressee (or authorized to receive for the addressee), you may not use, copy or disclose to anyone the message or any information contained in the message (including attachments). If you have received this message in error, please advise the sender by reply e-mail and delete the message. -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of D.Enrique ESCOBAR ESPINOZA Sent: Tuesday, August 22, 2006 9:22 AM To: James W. MacDonald; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] CEL.list may i haven t explained the things correctly may be because my mother tongue is spanish & my second one is french... you had a good idea, but the cel files i want can be in diferent directories, maybe i want to normalize (nrom) 10 hgu133a celfiles that are in 10 different paths or directories... Thanks --- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > Please don't reply just to me. The idea of a list is to keep the > questions and answers available for others as well. > > I don't understand your response. How does this duplicate data? > Also, > what is your 'norm'? > > My understanding of your original question was that you wanted to > operate on celfiles that are not in your working directory, which > is > what the celfile.path argument is for. Am I missing something? > > Best, > > Jim > > D.Enrique ESCOBAR ESPINOZA wrote: > > i don t want to duplicate data, > > my norm should be in another place than my cel files > > > > --- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > > > > > >>Hi Enrique, > >> > >>There is probably a way to use a file like that, but wouldn't it > be > >> > >>easier to just pass the path to your call to justRMA()? > >> > >>eset <- justRMA(celfile.path = > "/atlas/affy/proto_GQ/GQ005/M/20/") > >> > >>Best, > >> > >>Jim > >> > >> > >>D.Enrique ESCOBAR ESPINOZA wrote: > >> > >>>i have decided to read cel files from a list containing full > path > >> > >>to > >> > >>>each cel files, > >>>one per line: > >>>&$>head /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/CEL.list > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL > >>>in R console i ve done: > >>> > >>> > >>>>(cels =celslist ); > >>> > >>>[[1]] > >>>[1] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL" > >> > >>>[2] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL" > >> > >>>[3] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL" > >> > >>>[4] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL" > >> > >>>[5] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" > >> > >>>[6] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL" > >> > >>>[7] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" > >> > >>>[8] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" > >> > >>> > >>>>(cels1=celslist[[1]]); > >>> > >>>[1] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL" > >> > >>>[2] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL" > >> > >>>[3] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL" > >> > >>>[4] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL" > >> > >>>[5] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" > >> > >>>[6] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL" > >> > >>>[7] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" > >> > >>>[8] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" > >> > >>>in the fisrt caSE <(cels =celslist)> i have this error: > >>>Error in just.rma(filenames = l$filenames, phenoData = > >> > >>l$phenoData, > >> > >>>description = l$description, : > >>> Could not open file > >>> > >> > > > /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/c("/atlas/affy/proto_GQ/GQ00 5/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL", > > > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" > >>>in the last case <(cels1=celslist[[1]])> i ve this error: > >>>Error in just.rma(filenames = l$filenames, phenoData = > >> > >>l$phenoData, > >> > >>>description = l$description, : > >>> Could not open file > >>> > >> > > > /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2//atlas/affy/proto_GQ/GQ005/M /20/MG_U74Av2/GQ005M02D20M1-R0.CEL > > > >>>can someone tell me how to edit my CEL.list file in order to put > >> > >>1 > >> > >>>absolute path to each *.CEL and force R to normalize in the > >> > >>current > >> > >>>directory *.CEL that are in other directories? > >>> > >>>_______________________________________________ > >>>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 > >> > >> > >>-- > >>James W. MacDonald, M.S. > >>Biostatistician > >>Affymetrix and cDNA Microarray Core > >>University of Michigan Cancer Center > >>1500 E. Medical Center Drive > >>7410 CCGC > >>Ann Arbor MI 48109 > >>734-647-5623 > >> > >> > >>********************************************************** > >>Electronic Mail is not secure, may not be read every day, and > >>should not be used for urgent or sensitive issues. > >> > > > > > > > > -------------------------------------------------- > > D.Enrique ESCOBAR ESPINOZA > > (DESS Bioinfomatique > > B.Sc. Biologie Moleculaire > === message truncated === _______________________________________________ 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 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of D.Enrique ESCOBAR ESPINOZA Sent: Tuesday, August 22, 2006 9:22 AM To: James W. MacDonald; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] CEL.list may i haven t explained the things correctly may be because my mother tongue is spanish & my second one is french... you had a good idea, but the cel files i want can be in diferent directories, maybe i want to normalize (nrom) 10 hgu133a celfiles that are in 10 different paths or directories... Thanks --- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > Please don't reply just to me. The idea of a list is to keep the > questions and answers available for others as well. > > I don't understand your response. How does this duplicate data? > Also, > what is your 'norm'? > > My understanding of your original question was that you wanted to > operate on celfiles that are not in your working directory, which > is > what the celfile.path argument is for. Am I missing something? > > Best, > > Jim > > D.Enrique ESCOBAR ESPINOZA wrote: > > i don t want to duplicate data, > > my norm should be in another place than my cel files > > > > --- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > > > > > >>Hi Enrique, > >> > >>There is probably a way to use a file like that, but wouldn't it > be > >> > >>easier to just pass the path to your call to justRMA()? > >> > >>eset <- justRMA(celfile.path = > "/atlas/affy/proto_GQ/GQ005/M/20/") > >> > >>Best, > >> > >>Jim > >> > >> > >>D.Enrique ESCOBAR ESPINOZA wrote: > >> > >>>i have decided to read cel files from a list containing full > path > >> > >>to > >> > >>>each cel files, > >>>one per line: > >>>&$>head /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/CEL.list > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL > >>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL > >>>in R console i ve done: > >>> > >>> > >>>>(cels =celslist ); > >>> > >>>[[1]] > >>>[1] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL" > >> > >>>[2] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL" > >> > >>>[3] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL" > >> > >>>[4] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL" > >> > >>>[5] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" > >> > >>>[6] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL" > >> > >>>[7] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" > >> > >>>[8] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" > >> > >>> > >>>>(cels1=celslist[[1]]); > >>> > >>>[1] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL" > >> > >>>[2] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL" > >> > >>>[3] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL" > >> > >>>[4] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL" > >> > >>>[5] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" > >> > >>>[6] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL" > >> > >>>[7] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" > >> > >>>[8] > >> > >>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" > >> > >>>in the fisrt caSE <(cels =celslist)> i have this error: > >>>Error in just.rma(filenames = l$filenames, phenoData = > >> > >>l$phenoData, > >> > >>>description = l$description, : > >>> Could not open file > >>> > >> > > > /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/c("/atlas/affy/proto_GQ/GQ00 5/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL", > > > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL", > >>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" > >>>in the last case <(cels1=celslist[[1]])> i ve this error: > >>>Error in just.rma(filenames = l$filenames, phenoData = > >> > >>l$phenoData, > >> > >>>description = l$description, : > >>> Could not open file > >>> > >> > > > /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2//atlas/affy/proto_GQ/GQ005/M /20/MG_U74Av2/GQ005M02D20M1-R0.CEL > > > >>>can someone tell me how to edit my CEL.list file in order to put > >> > >>1 > >> > >>>absolute path to each *.CEL and force R to normalize in the > >> > >>current > >> > >>>directory *.CEL that are in other directories? > >>> > >>>_______________________________________________ > >>>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 > >> > >> > >>-- > >>James W. MacDonald, M.S. > >>Biostatistician > >>Affymetrix and cDNA Microarray Core > >>University of Michigan Cancer Center > >>1500 E. Medical Center Drive > >>7410 CCGC > >>Ann Arbor MI 48109 > >>734-647-5623 > >> > >> > >>********************************************************** > >>Electronic Mail is not secure, may not be read every day, and > >>should not be used for urgent or sensitive issues. > >> > > > > > > > > -------------------------------------------------- > > D.Enrique ESCOBAR ESPINOZA > > (DESS Bioinfomatique > > B.Sc. Biologie Moleculaire > === message truncated === _______________________________________________ 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

Ben may have a trick that will work, but I don't know of any way to get read.affybatch() to use an arbitrary set of directories for the celfiles. You could probably hack the code to do something like that pretty easily if you really wanted to. Best, Jim D.Enrique ESCOBAR ESPINOZA wrote: > may i haven t explained the things correctly > may be because my mother tongue is spanish & my second one is > french... > you had a good idea, but the cel files i want can be in diferent > directories, > maybe i want to normalize (nrom) 10 hgu133a celfiles that are in 10 > different paths or directories... > > Thanks > --- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > > >>Please don't reply just to me. The idea of a list is to keep the >>questions and answers available for others as well. >> >>I don't understand your response. How does this duplicate data? >>Also, >>what is your 'norm'? >> >>My understanding of your original question was that you wanted to >>operate on celfiles that are not in your working directory, which >>is >>what the celfile.path argument is for. Am I missing something? >> >>Best, >> >>Jim >> >>D.Enrique ESCOBAR ESPINOZA wrote: >> >>>i don t want to duplicate data, >>>my norm should be in another place than my cel files >>> >>>--- "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: >>> >>> >>> >>>>Hi Enrique, >>>> >>>>There is probably a way to use a file like that, but wouldn't it >> >>be >> >>>>easier to just pass the path to your call to justRMA()? >>>> >>>>eset <- justRMA(celfile.path = >> >>"/atlas/affy/proto_GQ/GQ005/M/20/") >> >>>>Best, >>>> >>>>Jim >>>> >>>> >>>>D.Enrique ESCOBAR ESPINOZA wrote: >>>> >>>> >>>>>i have decided to read cel files from a list containing full >> >>path >> >>>>to >>>> >>>> >>>>>each cel files, >>>>>one per line: >>>>>&$>head /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/CEL.list >>>>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL >>>>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL >>>>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL >>>>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL >>>>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL >>>>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL >>>>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL >>>>>/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL >>>>>in R console i ve done: >>>>> >>>>> >>>>> >>>>>>(cels =celslist ); >>>>> >>>>>[[1]] >>>>>[1] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL" >>>> >>>> >>>>>[2] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL" >>>> >>>> >>>>>[3] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL" >>>> >>>> >>>>>[4] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL" >>>> >>>> >>>>>[5] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" >>>> >>>> >>>>>[6] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL" >>>> >>>> >>>>>[7] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" >>>> >>>> >>>>>[8] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" >>>> >>>> >>>>>>(cels1=celslist[[1]]); >>>>> >>>>>[1] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL" >>>> >>>> >>>>>[2] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL" >>>> >>>> >>>>>[3] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL" >>>> >>>> >>>>>[4] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL" >>>> >>>> >>>>>[5] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" >>>> >>>> >>>>>[6] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL" >>>> >>>> >>>>>[7] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" >>>> >>>> >>>>>[8] >>>> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" >>>> >>>> >>>>>in the fisrt caSE <(cels =celslist)> i have this error: >>>>>Error in just.rma(filenames = l$filenames, phenoData = >>>> >>>>l$phenoData, >>>> >>>> >>>>>description = l$description, : >>>>> Could not open file >>>>> >>>> > /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/c("/atlas/affy/proto_GQ/GQ 005/M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL", > >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M02D20M1-R1.CEL", >> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03A20M1-R0.CEL", >> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03C20M1-R0.CEL", >> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL", >> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03E20M1-R0.CEL", >> >>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL", >>>> >>>>>"/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03G20M1-R0.CEL" >>>>>in the last case <(cels1=celslist[[1]])> i ve this error: >>>>>Error in just.rma(filenames = l$filenames, phenoData = >>>> >>>>l$phenoData, >>>> >>>> >>>>>description = l$description, : >>>>> Could not open file >>>>> >>>> > /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2//atlas/affy/proto_GQ/GQ005 /M/20/MG_U74Av2/GQ005M02D20M1-R0.CEL > >>>>>can someone tell me how to edit my CEL.list file in order to put >>>> >>>>1 >>>> >>>> >>>>>absolute path to each *.CEL and force R to normalize in the >>>> >>>>current >>>> >>>> >>>>>directory *.CEL that are in other directories? >>>>> >>>>>_______________________________________________ >>>>>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 >>>> >>>> >>>>-- >>>>James W. MacDonald, M.S. >>>>Biostatistician >>>>Affymetrix and cDNA Microarray Core >>>>University of Michigan Cancer Center >>>>1500 E. Medical Center Drive >>>>7410 CCGC >>>>Ann Arbor MI 48109 >>>>734-647-5623 >>>> >>>> >>>>********************************************************** >>>>Electronic Mail is not secure, may not be read every day, and >>>>should not be used for urgent or sensitive issues. >>>> >>> >>> >>> >>>-------------------------------------------------- >>>D.Enrique ESCOBAR ESPINOZA >>>(DESS Bioinfomatique >>>B.Sc. Biologie Moleculaire >> > === message truncated === > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.