[BioC] Normalising both Affy mogene 1.0 and 1.1 together

James W. MacDonald jmacdon at uw.edu
Mon May 19 15:58:54 CEST 2014


Hi Joel,

The short answer is that you can't. You can only process the two sets of 
arrays separately.

Best,

Jim


On 5/17/2014 9:08 AM, Joel Ma wrote:
> Hi
>
> I have two sets of data generated from Affymetrix mogene 1.0 ST and the Affmetrix mogene 1.1 ST Array. I am trying to normalise them together with the following but it did not work. How do you read two types of CEL files with identical gene lists but different chip dimensions?
>
>> library(oligo)
>> library(pd.mogene.1.0.st.v1)
>> library(pd.mogene.1.1.st.v1)
>> celFiles <- list.celfiles()
>> Rawdata <- read.celfiles(celFiles)
> All the CEL files must be of the same type.
> Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE
>
>
> Cheers
>
> Joel Z Ma, PhD
>
> Dept. of Microbiology and Immunology
> The Peter Doherty Institute for Infection and Immunity
> University of Melbourne
> 792 Elizabeth Street
> Parkville
> Victoria, 3000
>
> Ph: +61 3 83440775
> E-mail: jzma at unimelb.edu.au
>
>
>
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099



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