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I performed these remappings using data from our chip files for NCBI/Entrez Gene IDs, Ensembl Gene IDs, and Gene Symbols using functions in R. Not all probes have valid gene mappings, and so those probes would be discarded in the CHIP assembly. This is a common thing in old platforms as they were frequently constructed using the UniGene database as a reference which was based on old EST technologies that were quite noisy and imprecise.
If your dataset is already in Human Gene Symbols you *can* choose "No collapse" but unless your dataset was analyzed using the specific version of Ensembl/Gencode that we used when constructing that version of MSigDB we recommend using the "Human_Gene_Symbol_with_Remapping" chip as the chip platform as that will ensure that any obsolete symbols are converted to their current equivalents, otherwise genes with symbols that have changed will be lost from the analysis.
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
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