[BioC] load and normalize arrays from different platform

[Moshe Olshansky]

If you wish to normalize them together you can do what Jim suggested but
without normalization, get the two expression matrices, combine them
(using common genes only) and then use normalization functions from limma
to normalize the two sets together.

Regards,
Moshe.



> Hi Wendy,
>
> On 2/22/2011 3:13 PM, Wendy Qiao wrote:
>> Hi all,
>>
>> I need to load and normalize CEL files from two different platforms, one
>> platform is *U133AAofAv2 (22944 affyids)* and the other is *HG-U133A_2
>> (22277 affyids)*. I believe that these two platforms have very similar
>> annotations.
>
> They may have similar annotations, but you won't be able to load and
> normalize together. You are better off normalizing separately, and then
> if you need to analyze together, you can attempt to subset to the
> intersecting probesets and then do the analysis.
>
> Best,
>
> Jim
>
>
>>
>> When I read all the file together using ReadAffy, I got an error saying,
>>
>>> es.affy<-ReadAffy(filenames=celfile, celfile.path=celpath,
>>> phenoData=NULL)
>> Error in read.affybatch(filenames = l$filenames, phenoData =
>> l$phenoData,
>>   :
>>    Cel file XX does not seem to have the correct dimensions
>>
>> I figure that is because two platform has different cdf. So I tried to
>> change the cdf name for *U133AAofAv2 *using library("affxparser"). The I
>> got
>> the following errors,
>>
>>> convertCel(celfile, celfile.output, newChipType="HG-U133A_2")
>> Error in .unwrapDatHeaderString(header$DatHeader) :
>>    Internal error: Failed to extract 'pixelRange' and 'sampleName' from
>> DAT
>> header.  They became identical:   HG-U133A_2.1sq         
>>
>> I am not sure how to get around with this problem? Could anybody helps?
>> Or
>> what would be the best way to normalize two datasets like mine? Thank
>> you
>> very much. Any suggestion is appreciated.
>>
>>
>> Thank you very much,
>> Wendy
>>
>> 	[[alternative HTML version deleted]]
>>
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>
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-- 
Moshe Olshansky
Division of Bioinformatics
The Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052
e-mail: olshansky at wehi.edu.au
tel: (03) 9345 2697


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