[BioC] CEL.list

[James W. MacDonald]

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/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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-- 
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.