[BioC] Affy data

[James MacDonald]

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
> 
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> 
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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