To summarize multiple probe sets per gene, we used the default settings of the collapseRows R function [ 21].
For genes with multiple probe sets, in order to avoid overcounting, we chose the probe set with the lowest P-value.
On many Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver inconsistent or even contradictory measurements.
The array platform included probe sets corresponding to 19851 human genes, with most genes represented by multiple probe sets [40].
Certain transcripts correspond to multiple probe sets on the Affymetrix array.
In addition, in 32 instances there were multiple probe sets for the same gene.
In Affymetrix U133 microarray chips, many genes are represented by multiple probe sets.
To avoid biases, genes represented by multiple probe sets were counted only once.
For genes with multiple probe sets, the highest ratio was used.
The number of available 1-1 orthologene gene pairs was 7182, out of which 3142 had multiple probe sets.
Multiple probe sets from the same gene were grouped into a single datum when the expression was correlated (r>0.75).
