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