[BioC] Quantile normalization without using affyBatch

Shinhan Shiu shiu at uchicago.edu
Wed Apr 20 17:00:39 CEST 2005

Thanks for the comments, I used both approaches as suggested and they give 
the same values.

I have one more question regarding between array normalization. For the 
tiling array I am working on, there are several arrays with non-overlapping 
probes on them. As I understand, the between array normalization is 
generally applied to different hybridization experiments to the same kind 
of array. So, does it make sense to do between array normalization even 
though the sequences represented in the arrays are mostly different?

Best Regards,


At 01:07 PM 4/19/2005, Suresh Gopalan wrote:
>normalize.quantiles(matrixofvalues) should work.
>(Suresh Gopalan, PhD)
>----- Original Message ----- From: "Shinhan Shiu" <shiu at uchicago.edu>
>To: <bioconductor at stat.math.ethz.ch>
>Sent: Tuesday, April 19, 2005 12:52 PM
>Subject: [BioC] Quantile normalization without using affyBatch
>>I am working on Arabidopsis tiling array data. I want to adjust the 
>>intensity based on GC content then do normalization. But the CDF and CEL 
>>files are not available so the sequences and raw intensities are 
>>downloaded from Gene Expression Omnibus instead.
>>I have extracted codes from gcrma and the hacked version works fine for 
>>background correction and affinity adjustment. I run into trouble, 
>>however, when I try to do quantile normalization.
>>The method "normalize" takes an affyBatch object but I am working with a 
>>matrix of numbers. I wonder if there is any work around or other methods 
>>I can use.
>>  Shinhan Shiu
>>  Dept. of Ecology and Evolution
>>  University of Chicago
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch

  Shinhan Shiu
  Dept. of Ecology and Evolution
  University of Chicago

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