There were several ways in which I could normalize the data:
- Use Level 2 data from TCGA (somehow normalized by TCGA). No description of the methods was available at the time when I started the analyses. Presumably it was done in the same way as for the glioblastoma paper. TCGA's big paper on ovarian cancer just came out and I think they have some explanation how they did it. I haven't read it yet. Also, TCGA's advantage is that they have all Illumina control files from the arrays (hybridization, labeling, DNA concentration) and they didn't upload them to the central repository. Their clinical files don't include this technical information or it is ambiguous. However, they definitely have useful information in their paper such as excluding the stage I patients because they might be very different from any other OC patients.
- Second method is to use normalization approaches implemented in Bioconductor lumi package. They offer quantile normalization for color balance adjustment and for the normalization between patients forcing everything to be "the same". Here are a few images from the normalization (I collected level 1 data, extracted )