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All the statistical analyses described below use the normalized data sets.
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For the comparison of Affymetrix and Agilent platforms, we used the normalized data from test site 2, which was normalized using PLIER [37].
The final training data sets used for learning the classification/estimation models are created using the normalized data for the VDP and VH classes. .
The final training input data sets used for learning the classification/estimation models are created using the normalized data for all the classes considered.
The correlation matrix (340,000×340,000) was computed using the normalized data set.
As raw data are only available for some of the microarray datasets, we used the "normalized" data provided by submitters.
We used the normalized data set.
SAM analyses were performed using Flexarray software using the normalized data of the 45,000 probesets.
Both analyses resulted in the highest percentages in the peaks called using the normalized data sets.
Using the normalized data, we revisited the preferential interactions originally described between subsets of discrete chromosomal features.
The Spearman's correlation coefficient was further calculated for each gene using the normalized data to quantify the consistency between the Solexa sequencing and RT-qPCR experiments.
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