The background estimation and the probe summarization were done on the raw data from each chipset separately according to the RMA algorithm [34].
Arrays were normalized using Quantile normalization and probeset summarization was done using Median Polish.
Probeset summarization was done using ExonRMA16 algorithm with confidence level set at 100%.
Data collation and summarization was done in two steps, as recommended methodological procedures found in the literature [ 38, 40].
Preparation was done in R. All Affymetrix data sets except GSE4732_p1 were processed with the affy package [ 34] from raw data, and expression summarization was done with the rma algorithm [ 35] with quantile normalization.
In brief, RMA summarization of probe level data is done by performing three individual treatments on all of the experimental CEL data simultaneously.
In fact, we're going to make a general summarization: TiVo is doing better than analysts thought it would, and that's because it's concentrating on working with content providers, not just using what they create.
Further statistical analysis and summarization needs to be done before this data can be leveraged.
Operationalizing the points-of-view coverage of the summarization process can be done in one of two ways.
