Quantile normalization without using affyBatch
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Shinhan Shiu ▴ 60
@shinhan-shiu-1172
Last seen 9.6 years ago
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 ******************************** Shinhan Shiu Dept. of Ecology and Evolution University of Chicago
Normalization cdf gcrma Normalization cdf gcrma • 1.1k views
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@james-w-macdonald-5106
Last seen 7 hours ago
United States
Shinhan Shiu wrote: > 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. How about normalizeBetweenArrays() in the limma package? Jim > > Shinhan > > > ******************************** > Shinhan Shiu > Dept. of Ecology and Evolution > University of Chicago > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 9.6 years ago
> 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. normalize.quantiles() operates directly on a matrix by quantile normalizing columns.
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@suresh-gopalan-932
Last seen 9.6 years ago
normalize.quantiles(matrixofvalues) should work. Suresh (Suresh Gopalan, PhD) ----- Original Message ----- From: "Shinhan Shiu" <shiu@uchicago.edu> To: <bioconductor@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 > > > ******************************** > Shinhan Shiu > Dept. of Ecology and Evolution > University of Chicago > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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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, Shinhan At 01:07 PM 4/19/2005, Suresh Gopalan wrote: >normalize.quantiles(matrixofvalues) should work. > >Suresh > >(Suresh Gopalan, PhD) >----- Original Message ----- From: "Shinhan Shiu" <shiu@uchicago.edu> >To: <bioconductor@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 >> >> >>******************************** >> Shinhan Shiu >> Dept. of Ecology and Evolution >> University of Chicago >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > ******************************** Shinhan Shiu Dept. of Ecology and Evolution University of Chicago
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