Re: [aroma.affymetrix] Relative Copy Number Analysis

Hi Dario, Pierre Neuvial has kindly provided a more up-to-date vignette for doing paired total copy number analysis. You find it at: http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis See if that helps /Henrik On Wed, Sep 22, 2010 at 5:05 PM, Dario Strbenac

[aroma.affymetrix] Multiple NUSE and RLE Plots?

Hi All, I'm using aroma to analyze CEL files from 141 SNP 6.0 arrays. I fit the quality assessment model as follows: plm = RmaPlm(csR) fit(plm, verbose = log) qam = QualityAssessmentModel(plm) Then I'd like to produce NUSE and RLE plots for 10 arrays at a time. Can someone please tell me how

[aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....

Hi All, I am trying to normalize a mouse exon array dataset using GCRMA normalization technique. I have exactly followed all the necessary steps for storing the dataset and the cdf file. the code and the output I am using are as follows: source(http://aroma-project.org/hbLite.R;);