[BioC] Best way to import GCOS tab-delimited life

[Sean Davis]

On Thursday 01 March 2007 06:48, Daniel Brewer wrote:
> Sean Davis wrote:
> > On Thursday 01 March 2007 05:31, Daniel Brewer wrote:
> >> What is the best way to import (what I believe is) a Affymetrix GCOS
> >> produced tab-delimited results file for use with limma and the like?
> >>
> >> Unfortunately I do not have access to the CEL files.
> >
> > I'm not sure what format the files are, but you might want to look at
> > read.maimages() in the limma package.  Alternatively, you can use
> > read.table for each array and then put the columns together any way you
> > like using R commands.  There might be better ways, besides the two
> > mentioned here.
> >
> > Sean
>
> Thanks.
>
> Just for completeness, here is the first couple of lines of one of the
> files:
> 	Descriptions	Met 1_Signal	Met 1_Detection	Met 1_Detection p-value	Met
> 2_Signal	Met 2_Detection	Met 2_Detection p-value	Met 3_Signal	Met
> 3_Detection	Met 3_Detection p-value	Met 4_Signal	Met 4_Detection	Met
> 4_Detection p-value	Met 5_Signal	Met 5_Detection	Met 5_Detection
> p-value	Met 6_Signal	Met 6_Detection	Met 6_Detection p-value	Met
> 7_Signal	Met 7_Detection	Met 7_Detection p-value	Met 8_Signal	Met
> 8_Detection	Met 8_Detection p-value
> AFFX-BioB-5_at	"J04423 E coli bioB gene biotin synthetase  (-5, -M, -3
> represent transcript regions 5 prime, Middle, and 3 prime
> respectively)"	624.4	P	0.002275	955.7	P	0.000857	629.5	P	0.002275
> 819.4	P	0.000972	456.4	P	0.001593	498	P	0.002275	470.7	P	0.002275
> 1141.6	P	0.000509

So, just read this with read.table().  Then, you can get various matrices like 
so:

dat <- read.table(....)

signalMatrix <- as.matrix(dat[,seq(2,ncol(dat),3)]) # extract every third 
column starting with the second column
detectionMatrix <- as.matrix(dat[,seq(3,ncol(dat),3]) # And start with the 
third column, etc.
....

You can use these matrices to make whatever data structure you like, or just 
use the matrix directly with limma.

Sean