[BioC] load and normalize arrays from different platform

[James W. MacDonald]

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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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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