Question: How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
gravatar for Chanchal Kumar
11.2 years ago by
Chanchal Kumar130 wrote:
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 Phone: (Office) +49 (0) 89 8578 2296 Fax:(Office) +49 (0) 89 8578 2219 ===============================
proteomics hgu95av2 gseabase • 511 views
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