[BioC] CEL.list

[James W. MacDonald]

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?
> 
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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


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