Hi Jim,

Thanks !

Further, I'm eagerly looking forward to comment(s) on the methods of
integrating those separately processed and analyzed data, as you have
mentioned.
[Else, pointers towards some ref. would also be helpful]

kathy





On Sat, Apr 12, 2008 at 1:38 AM, James MacDonald <jmacdon@med.umich.edu>
wrote:

> Hi Kathy,
>
> The different chip types will have to be processed and analyzed
> separately. The easiest way to do so is to make separate subdirectories and
> put the different chip types in their own directory.
>
> Best,
>
> Jim
>
>
>
> Kathy Duncan wrote:
>
> > Hi All,
> >
> > I've got an Affymetrix dataset which I need to process and finally get
> > the
> > list of genes and their respective expression levels. Without having
> > much
> > prior idea and experience, I tried the ReadAffy() function within the
> > directory containing the .CEL files and I came across the error saying :
> >
> > Error in read.affybatch(filenames = l$filenames, phenoData =
> > l$phenoData,  :
> >
> >  Cel file MN.CEL does not seem to have the correct dimensions
> >
> > Then I tried the following command for each individual .CEL files of
> > that
> > investigation (as I am not sure how to get such information about all
> > the
> > files using a single command):
> >
> > whatcdf ("filename", compress = getOption("BioC")$affy$compress.cel)
> >
> > I could see that the investigation is referring to different CDF files.
> >
> > Could you please inform me how I should proceed !
> >
> > kathy
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > Bioconductor@stat.math.ethz.ch
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> > Search the archives:
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> >
>
> --
> James W. MacDonald, MS
> Biostatistician
> UMCCC cDNA and Affymetrix Core
> University of Michigan
> 1500 E Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>

	[[alternative HTML version deleted]]

