[BioC] CEL.list vol 2

[Ben Bolstad]

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?
> 
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-- 
Ben Bolstad <bmb at bmbolstad.com>
http://bmbolstad.com