[BioC] Specifying Sample Names in ReadAffy;

[Paul Boutros]

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

----------------------------------------
This mail sent through www.mywaterloo.ca