How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
0
0
Entering edit mode
@chanchal-kumar-2465
Last seen 7.4 years ago
Dear All, I have a set of Entrez ids which have been ordered as per fold change expression from a control experiment. I am now interested in carrying out gene set enrichment analysis using Bioconductor GSEABase package. I don't have any other statistics for these genes. Is it possible to carry out GSEA on a vector of Entrezids which is ordered by say fold change? I attach an example vector and would like to carry out GSEA on this test set to get an idea of how this might work. library(annotate) library(hgu95av2.db) set.seed(12345) set1 <- unique(getEG(sample(ls(hgu95av2GO), 100), "hgu95av2")) set1<-na.omit(set1) # as I get NAs in the vector before For GSEA I assume that element set1[1] has highest fold change and set1[length(set1)] has the lowest fold change. Any help in this regard will be appreciated. Thanks in advance! ---------------------------------------------------------------------- -- --------------- > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y= German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] annotate_1.18.0 xtable_1.5-2 hgu95av2.db_2.2.0 [4] AnnotationDbi_1.2.1 RSQLite_0.6-8 DBI_0.2-4 [7] Biobase_2.0.1 loaded via a namespace (and not attached): [1] splines_2.7.0 ---------------------------------------------------------------------- -- --------------- Best Regards, Chanchal =============================== Chanchal Kumar, Ph.D. Candidate Dept. of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 D-Martinsried (near Munich) Germany e-mail: chanchal at biochem.mpg.de Phone: (Office) +49 (0) 89 8578 2296 Fax:(Office) +49 (0) 89 8578 2219 http://www.biochem.mpg.de/mann/ ===============================
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase • 685 views
ADD COMMENT

Login before adding your answer.

Traffic: 470 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6