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

[Daniel Brewer]

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

-- 
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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