Just a follow up: The 'HG-U133A_2' chip type is a *physically different* array than the 'HT_HG-U133A' chip type (aliased 'U133AAofAv2' during its early-access stage). For instance, the former has 732x732 probes whereas the latter has 744x744 probes, cf. http://www.aroma-project.org/chipTypes/ In other words, the problem is *not* just about different chip type *aliases* (as it would have been if you had CEL files labelled 'HT_HG-U133A' and ''U133AAofAv2' when you theoretically can treat all to be of the same chip type). You need to proceed as others have already suggested in this thread. /Henrik On Tue, Feb 22, 2011 at 5:02 PM, Moshe Olshansky <olshansky at="" wehi.edu.au=""> wrote: > 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]] >> _______________________________________________ >> >>> Bioconductor >>> mailing list >> Bioconductor at r-project.org >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the >>> archives: >>> >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> -- >>> > 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 > >>> ********************************************************** > Electronic >>> Mail >>> is not secure, may not be read every day, and should not > be used for >>> urgent or sensitive issues > >>> _______________________________________________ >>> > Bioconductor mailing list > Bioconductor at r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the >>> archives: >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor >>> 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 >>> ______________________________________________________________________ >>> The >>> information in this email is confidential and intended solely for the >>> addressee. 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