This tool takes a normalized dataset, and combines all probes that have been mapped to the same gene name into a single expression estimate for that gene. Probes are averaged together to get a single estimate of expression.
Please note, that summarizing multiple probes for a given gene (or multiple probe-sets for an Affy array) is not recommended as a routine procedure by any of the Bioconductor software developers. By combining the expression information you lose the probe/probeset wise information resulting for example from different isoforms being present in the samples.
Note that some of the pathway analysis tools require the probe IDs to work -you can however use "Hypergeometric test for ConsensusPathDB" as it supports any data with gene symbols.
A new, smaller dataset with only one expression value per gene per sample.