Help for error 1005

[롱숏]

GNLY 0.457 10.433
FXYD2 1.467 0.063
KLRC1 0.083 1.277
LINC02446 0.051 0.942
DPP4 0.005 0.222
TRDV2 0.368 4.335
TRDV1 2.676 0.189
ZNF683 0.293 3.211
HAVCR2 0.376 0.018
TRAV38-2DV8 0.877 0.017
TMEM155 0.251 0.007
PMCH 0.356 0.007
DRAIC 0.216 0.011

Error is 1005 and I choose ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_ILLUMINA_Array_MSigDB.v2023.1.Hs.chip
How can i choos appropriate chip?

[Castanza, Anthony]

Hello,

These appear to be Human Gene Symbols, so the Human Gene Symbol with Remapping CHIP file should be used here.
Additionally, it looks like you only have two samples included in the example you sent, so you may have to change some other GSEA metrics in order to get it to work such as the permutation mode (you might need gene set permutation) and metric for ranking genes you might need log2_ratio_of_classes).

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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