[BioC] CEL.list

Hassane, Duane Duane_Hassane at URMC.Rochester.edu
Tue Aug 22 16:38:14 CEST 2006 

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


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-----Original Message-----
From: bioconductor-bounces at 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/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 ===

_______________________________________________
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 at 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/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 ===

_______________________________________________
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

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