[BioC] load and normalize arrays from different platform

[Moshe Olshansky]

Hi Wendy,

Just one more comment: since you are using two different platforms you
should expect batch effect, so it is important to normalize the two
batches together (and there are several ways of doing this). Even then
check your normalized expression values to see whether you still have
batch effect.

Moshe.

> 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 at 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
>> 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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>> 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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