_1.2        httr\_1.3.1             fgsea\_1.6.0            acepack\_1.4.1          pkgconfig\_2.0.1        nnet

nbsp;        \[15\] bitops\_1.0-6             fgsea\_1.0.2               \[17\] assertthat\_0.2.0         scales\_0.4.1     &nbsp

I have problems with the geneList argument for the enrichment Analysis of clusterprofiler. The example GeneList from the DOSE package shows a descending ordered vector of logFC with entrezID as names(). If I try to construct that from my toptable output I face a problem because several different probenames match the same entrezID which results in an error when I try to assign entrezID row.na…

I have a question for fgseaMultiLevel, when using the geneSets from msigdb, Homo sapiens: C2 category, should I filter the gene sets with respect to the genes present in my dataset using > filtered_geneSets93 <- lapply(geneSets, function(geneSet) {intersect(geneSet, unique_gene_ids93) }) where unique_gene_ids93 is the list of all the ensemble gene ids present in my counts matrix. Because …

Hi, it seems that I can't download fgsea_1.20.0.tar.gz. Tried both from R v4.1.0 and from web browser (https://bioconductor.org/packages/3.14/bioc/html/fgsea.html; with different web browsers, different OS, different connections: no access to the file). Is it just me? Could anyone check and suggest a solution? Thank you for the help. ```r # include your problematic code here with any cor…