Hi Moshe and James,

Thank you very much for your suggestions. They make sense. I will do that.

Regards,
Wendy



On 22 February 2011 19:27, Moshe Olshansky <olshansky@wehi.edu.au> wrote:

> 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
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