lets say that i want to work with *.CEls files that are par of an experiment: >getwd() >/atlas/affy/experiments/telomerase/ lets say that i m gathering .CELs in differents paths like this: /atlas/affy/proto_GQ/GQ005/M/14/MG_U74Av2/GQ005M03C14M1-R0.CEL /atlas/affy/proto_GQ/GQ005/M/16/MG_U74Av2/GQ005M03D16M1-R0.CEL /atlas/affy/proto_GQ/GQ005/M/18/MG_U74Av2/GQ005M03E18M1-R0.CEL /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL /atlas/affy/proto_GQ/GQ006/F/14/MG_U74Av2/GQ006M03C14F1-R0.CEL /atlas/affy/proto_GQ/GQ006/F/16/MG_U74Av2/GQ006M03D16F1-R0.CEL /atlas/affy/proto_GQ/GQ006/F/18/MG_U74Av2/GQ006M03E18F1-R0.CEL /atlas/affy/proto_GQ/GQ006/F/20/MG_U74Av2/GQ006M03F20F1-R0.CEL and i decide to put all the paths in a CEL.list in the curretn directory: /atlas/affy/experiments/telomerase/ and its absolute path is /atlas/affy/experiments/telomerase/CEL.list I want to save my Rdatas and all analysis in /atlas/affy/experiments/telomerase/ > # load my cels > celslist<- scan(file="CEL.list",what=list("c"),sep="\n",quiet=TRUE); > (cels =celslist ); [[1]] [1] "/atlas/affy/proto_GQ/GQ005/M/14/MG_U74Av2/GQ005M03C14M1-R0.CEL" [2] "/atlas/affy/proto_GQ/GQ005/M/16/MG_U74Av2/GQ005M03D16M1-R0.CEL" [3] "/atlas/affy/proto_GQ/GQ005/M/18/MG_U74Av2/GQ005M03E18M1-R0.CEL" [4] "/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" [5] "/atlas/affy/proto_GQ/GQ006/F/14/MG_U74Av2/GQ006M03C14F1-R0.CEL" [6] "/atlas/affy/proto_GQ/GQ006/F/16/MG_U74Av2/GQ006M03D16F1-R0.CEL" [7] "/atlas/affy/proto_GQ/GQ006/F/18/MG_U74Av2/GQ006M03E18F1-R0.CEL" [8] "/atlas/affy/proto_GQ/GQ006/F/20/MG_U74Av2/GQ006M03F20F1-R0.CEL" > (cels1=celslist[[1]]); [1] "/atlas/affy/proto_GQ/GQ005/M/14/MG_U74Av2/GQ005M03C14M1-R0.CEL" [2] "/atlas/affy/proto_GQ/GQ005/M/16/MG_U74Av2/GQ005M03D16M1-R0.CEL" [3] "/atlas/affy/proto_GQ/GQ005/M/18/MG_U74Av2/GQ005M03E18M1-R0.CEL" [4] "/atlas/affy/proto_GQ/GQ006/F/14/MG_U74Av2/GQ006M03C14F1-R0.CEL" [5] "/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" [6] "/atlas/affy/proto_GQ/GQ006/F/16/MG_U74Av2/GQ006M03D16F1-R0.CEL" [7] "/atlas/affy/proto_GQ/GQ006/F/18/MG_U74Av2/GQ006M03E18F1-R0.CEL" [8] "/atlas/affy/proto_GQ/GQ006/F/20/MG_U74Av2/GQ006M03F20F1-R0.CEL" when i do eset <-just.rma(filenames = cels , phenoData =NULL) eset1 <-just.rma(filenames = cels1, phenoData =NULL) i always receive >Error in just.rma(filenames = l$filenames, phenoData = >l$phenoData, >description = l$description, : > Could not open file what can i do for putting in filenames the correct different path foreach different .CEL?

I want to avoid clogging this list with endlessly answering repeating variations of this question (of which you have had several and re- asking again will probably just get you ignored). So here are the rules of the game as I see them. 1. Always use justRMA() or ReadAffy() (do not directly call just.rma or read.affybatch, these are not really meant to be called by the user) 2. If you decide that you want to append the full path to each file name eg my.cel.names <- c("/path/to/first.CEL","/Another/path/to/second.CEL") then 2.a if using justRMA() your call would be my.eset <- justRMA(filenames=my.cel.names,celfile.path="") 2.b if using ReadAffy() your call would be my.abatch <- ReadAffy(filenames=my.cel.names) 3. If you want to read all the cel files in a specified set of directories eg. my.cel.paths <- c("/path/to/group1/","/path/to/group2") then 3.a if using justRMA() your call would be my.eset <- justRMA(celfile.path=my.cel.paths) 3.b if using ReadAffy() your call would be my.abatch <- ReadAffy(celfile.path=my.cel.paths) 4. All the above is irrespective of your current working directory. 5. If you call ReadAffy() or justRMA() without arguments eg my.eset <- justRMA() my.abatch <- ReadAffy() in this case and only this case will it read the cel files in the current working directory. On Tue, 2006-08-22 at 09:02 -0700, D.Enrique ESCOBAR ESPINOZA wrote: > lets say that i want to work with *.CEls files that are par of an > experiment: > >getwd() > >/atlas/affy/experiments/telomerase/ > > lets say that i m gathering .CELs in differents paths like this: > /atlas/affy/proto_GQ/GQ005/M/14/MG_U74Av2/GQ005M03C14M1-R0.CEL > /atlas/affy/proto_GQ/GQ005/M/16/MG_U74Av2/GQ005M03D16M1-R0.CEL > /atlas/affy/proto_GQ/GQ005/M/18/MG_U74Av2/GQ005M03E18M1-R0.CEL > /atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL > /atlas/affy/proto_GQ/GQ006/F/14/MG_U74Av2/GQ006M03C14F1-R0.CEL > /atlas/affy/proto_GQ/GQ006/F/16/MG_U74Av2/GQ006M03D16F1-R0.CEL > /atlas/affy/proto_GQ/GQ006/F/18/MG_U74Av2/GQ006M03E18F1-R0.CEL > /atlas/affy/proto_GQ/GQ006/F/20/MG_U74Av2/GQ006M03F20F1-R0.CEL > > and i decide to put all the paths in a CEL.list > in the curretn directory: > /atlas/affy/experiments/telomerase/ > and its absolute path is > /atlas/affy/experiments/telomerase/CEL.list > > I want to save my Rdatas and all analysis in > /atlas/affy/experiments/telomerase/ > > > # load my cels > > celslist<- > scan(file="CEL.list",what=list("c"),sep="\n",quiet=TRUE); > > (cels =celslist ); > [[1]] > [1] "/atlas/affy/proto_GQ/GQ005/M/14/MG_U74Av2/GQ005M03C14M1-R0.CEL" > [2] "/atlas/affy/proto_GQ/GQ005/M/16/MG_U74Av2/GQ005M03D16M1-R0.CEL" > [3] "/atlas/affy/proto_GQ/GQ005/M/18/MG_U74Av2/GQ005M03E18M1-R0.CEL" > [4] "/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03F20M1-R0.CEL" > [5] "/atlas/affy/proto_GQ/GQ006/F/14/MG_U74Av2/GQ006M03C14F1-R0.CEL" > [6] "/atlas/affy/proto_GQ/GQ006/F/16/MG_U74Av2/GQ006M03D16F1-R0.CEL" > [7] "/atlas/affy/proto_GQ/GQ006/F/18/MG_U74Av2/GQ006M03E18F1-R0.CEL" > [8] "/atlas/affy/proto_GQ/GQ006/F/20/MG_U74Av2/GQ006M03F20F1-R0.CEL" > > (cels1=celslist[[1]]); > [1] "/atlas/affy/proto_GQ/GQ005/M/14/MG_U74Av2/GQ005M03C14M1-R0.CEL" > [2] "/atlas/affy/proto_GQ/GQ005/M/16/MG_U74Av2/GQ005M03D16M1-R0.CEL" > [3] "/atlas/affy/proto_GQ/GQ005/M/18/MG_U74Av2/GQ005M03E18M1-R0.CEL" > [4] "/atlas/affy/proto_GQ/GQ006/F/14/MG_U74Av2/GQ006M03C14F1-R0.CEL" > [5] "/atlas/affy/proto_GQ/GQ005/M/20/MG_U74Av2/GQ005M03D20M1-R0.CEL" > [6] "/atlas/affy/proto_GQ/GQ006/F/16/MG_U74Av2/GQ006M03D16F1-R0.CEL" > [7] "/atlas/affy/proto_GQ/GQ006/F/18/MG_U74Av2/GQ006M03E18F1-R0.CEL" > [8] "/atlas/affy/proto_GQ/GQ006/F/20/MG_U74Av2/GQ006M03F20F1-R0.CEL" > > when i do > eset <-just.rma(filenames = cels , phenoData =NULL) > eset1 <-just.rma(filenames = cels1, phenoData =NULL) > > i always receive > >Error in just.rma(filenames = l$filenames, phenoData = > >l$phenoData, > >description = l$description, : > > Could not open file > > > what can i do for putting in filenames > the correct different path foreach different .CEL? > > _______________________________________________ > 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 Bolstad <bmb at="" bmbolstad.com=""> http://bmbolstad.com