[BioC] Affy data

[James W. MacDonald]

Hi Kathy,

Assuming the chips are all the same species, I would probably use 
something like MergeMaid. There may be others -- you can check here:

http://bioconductor.org/packages/2.2/DifferentialExpression.html

Best,

Jim



Kathy Duncan wrote:
> 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 at med.umich.edu 
> <mailto:jmacdon at 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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> 
>     -- 
>     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
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623