[BioC] RE: Specifying Sample Names in ReadAffy (Correction)

[Paul Boutros]

Rafael pointed out that there was a typo in my example.  The correct version
is below:

> samples.files <- c(
	"RAE230A_043003_IM01T_LH.CEL",
	"RAE230A_043003_IM02T_LH.CEL",
	"RAE230A_043003_IM03T_LH.CEL",
	"RAE230A_043003_IM04T_LH.CEL",
          );

> samples.names <- c(
	"LET",
	"LEC",
	"WWT",
	"WWC",
          );

> Data <- ReadAffy(
	filenames = samples.files,
	sampleNames = samples.names
	);


> -----Original Message-----
> From: Paul Boutros [mailto:pcboutro at engmail.uwaterloo.ca]
> Sent: Friday, July 04, 2003 5:37 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: Specifying Sample Names in ReadAffy;
>
>
> Hello all,
>
> I would like to be able to specify the sampleNames parameter to
> ReadAffy to
> ease later parsing and analysis of the data somewhat.  The documentation
> (Textual description of affy vignete and ?ReadAffy) indicates
> that I need to
> set up a character array with both the file-names and the desired sample-
> names.  This is what I have used (limited data-set for testing):
>
> > samples.files <- c(
> 	"RAE230A_043003_IM01T_LH.CEL",
> 	"RAE230A_043003_IM02T_LH.CEL",
> 	"RAE230A_043003_IM03T_LH.CEL",
> 	"RAE230A_043003_IM04T_LH.CEL",
>           );
>
> > samples.names <- c(
> 	"LET",
> 	"LEC",
> 	"WWT",
> 	"WWC",
>           );
>
> > Data <- ReadAffy(
> 	filenames = samples.files);
> 	sampleNames = samples.animals,
> 	);
>
> But this fails with the error:
>
> Error in sub(pattern, replacement, x, ignore.case, extended) :
>         invalid argument
> In addition: Warning message:
> sampleNames not same length as filenames. Using filenames as
> sampleNames instead
>  in: ReadAffy(filenames = samples.files, sampleNames = samples.animals,
>
> So I tested:
> > length(samples.files);
> [1] 4
> > length(samples.names);
> [1] 4
>
> Have I misunderstood the purpose of the sampleNames argument?  Or
> ss there
> another way of changing the "column" names in an eSet and in
> write.exprs()
> output?
>
> Any suggestions much appreciated!
> Paul
>
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