[BioC] CEL.list

[Ben Bolstad]

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/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 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 ===
> 
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