how to choose the gene sets database and chip platform

[xiangrong chen]

Hi everyone,

Now I am using the GSEA to analyze the genes of the HepG2 cell, and I have the error: the collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub/gsea/annotations_versioned/Human_ENSEMBL_Gene_ID_MSigDB.v7.5.1.chip

could anyone tell me how to choose the gene sets database and chip platform? Thanks so much!

[Anthony Castanza]

Hello,

 

The chip platform you selected is indented for data where the gene identifiers are in human gene ID format as specified by Ensembl, this format looks like ENSG0000012345. If your identifiers do not look like this, then this is not the correct chip file for your data. Note that sometimes Ensembl Gene IDs have a version suffix, i.e. ENSG0000012345.6 these decimal versions would need to be discarded if they are present in your data.

 

Otherwise, you can send us a sampling of the identifiers in your file and we might be able to identify which chip file should be used.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/2cb297ab-03ae-462d-93b7-1b29468ea614n%40googlegroups.com.