[BioC] Normalising both Affy mogene 1.0 and 1.1 together

Steve Piccolo stephen.piccolo at hsc.utah.edu
Mon May 19 17:03:00 CEST 2014


Hi Joel,

You might try the SCAN() function in the SCAN.UPC package for this. You
can pass it a wildcard specifying the location of the CEL files, and it
will normalize them separately and then merge them based on overlapping
features. I haven¹t tried the exact thing you¹re describing, but it should
work. Let me know if it doesn¹t.

Regards,
-Steve


On 5/18/14, 4:00 AM, "bioconductor-request at r-project.org"
<bioconductor-request at r-project.org> wrote:

>Date: Sat, 17 May 2014 13:08:54 +0000
>From: Joel Ma <jzma at unimelb.edu.au>
>To: "bioconductor at r-project.org" <bioconductor at r-project.org>
>Subject: [BioC] Normalising both Affy mogene 1.0 and 1.1 together
>Message-ID:
>	<AB356226B32DE84F818CBA2CFC4BEE335F30D889 at 000S-EX-MBX-QS3.unimelb.edu.au>
>	
>Content-Type: text/plain
>
>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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