[aroma.affymetrix] Extract raw data for core transcripts from EXON arrays

Hi All, I have been looking at extracting raw data for core transcripts from HuEx-1_0-st-v2 chip type. I have downloaded the custom CDF file provided in http://www.aroma-project.org/node/122. chipType <- "HuEx-1_0-st-v2" cdf <- AffymetrixCdfFile$byChipType(chipType, tags="core") print(cdf) Affyme

[aroma.affymetrix] Re: Re-run aroma.affymetrix

Hi Mark, Thanks for your suggestions. What I have tried so far is: I removed all outliers CEL files from rawData and re-run the analysis. I was expecting a slightly different intensity distributions of chips (due to quantile normalization) but it seems I have the same distributions that I got with