Bioconductor Forum

Hello all, I was trying to perform GSEA for a dataset using the `fgsea` R package. The code I used was `fgseaRes <- fgsea(pathways = pathways, stats = ranks, minSize = 5, maxSize = Inf)` I received an warning

fgsea

updated 2.4 years ago • zli1

Running into an error of not being able to install or run fgsea in R Version 1.4.1106. ``` # library(fgsea) Error: package or namespace load failed for ‘fgsea’ in loadNamespace(i, c(lib.loc, .libPaths...vI[[i]]): there is no package called ‘fastmatch’ In addition: Warning message: package ‘fgsea’ was built under R version 4.1.1 #install.packages("fgsea", repos="http://cran.rstudio.com/"…

r fgsea

updated 20 months ago • amir.khan

Hi everyone I dont really have problems running fgsea itself but im trying to understand what gseaparam argument in fgsea() means. The vignette says it's a GSEA weight parameter...but weightage of what? each fgsea term? and to what exactly hope to hear some clarifications; tried googling it's still not clear to me

fgsea

updated 3.3 years ago • kavator

Hi All i ran fgsea() successfully; my sample is brain tissue but im getting quite a few fgsea GO hits that describe other relatively far off...tissues processes -like digestive system.. etc. i was wondering if there's a possibility to run my fgsea just on brain related GO processes? would appreciate any advice

fgsea

updated 10 months ago • kavator

Hello everyone, Back in October I performed fgsea analysis without problem, obtaining up/downregulated genesets. Now I am trying to do another analysis with fgsea, and...msigdbr_list <- split(x = msig$gene_symbol, f = msig$gs_name) #Running fgsea algorithm: fgseaRes <- fgseaMultilevel(pathways = msigdbr_list, stats = ranks) R version 4.1.3 (2022-03-10…

fgsea

updated 18 months ago • Barista

I can use GSEA to compare two datasets ([link to GSEA FAQ on how to do this][1]). I found `fgsea` package that can do GSEA calculation with pathways but I cannot figure out how to use this package to do the two datasets

GSEA fgsea

updated 9 weeks ago • Cen

Hi, I'm trying out the `` fgsea `` package, which is a great improvement over other much slower `` gsea `` implementations.   One question though - I'm interested...code> data(examplePathways)<br/>   data(exampleRanks)</code> <code>  fgseaDnRes <- fgsea(pathways = examplePathways,stats = exampleRanks,minSize=15,maxSize=500,nperm=10000)&l…

fgsea gsea

updated 6.7 years ago • rubi

Hi,   Does fgsea order the stats argument? What I'm currently doing is order ordering the effect (i.e. log treatment vs. control fold...changes) but their p-vaiues and passing that to fgsea. But the fgsea code suggests it re-ranks stats so the p-value ranking is lost. Is that the case? and if so is there any way to

fgsea

updated 6.3 years ago • rubi

biocLite command and am currently running it in R version 3.3.3 “Another Canoe.” When running the fgsea command the algorithm runs quickly (less than 1 second) for any number of permutations less than 1000, only taking 1.46

fgsea gsea

updated 6.2 years ago • shawn.w.foley

results table with such metrics with LFC, p.adf (or FDR) and etc. I wonder should I use in fgsea analysis all genes with estimated LFC values (from results table) or is it better to restrict set by p.adj (or FDR) < 0.05

fgsea

updated 2.5 years ago • alexandr.gopanenko

how does shrinking affects those values in stat column Additionally; i dont get why does fgsea uses stat column (whose values are presumably not affected by lfc shrink) instead of a shrunken column of values

fgsea DESeq2

updated 2.6 years ago • kavator

Hi there guys. I have gene expression data collected from nCounter with a panel of around 700 genes (Pancancer immune profiling panel). I performed differential expression analysis and now I want to see which immune-related pathways are over or under expressed in my samples. In my nCounter samples I do not have normal tissue so I can´t perform a differential expression analysis between tumor an…

NanoStringDiff clusterProfiler fgsea

updated 3 months ago • pg45863

I try to run an fgsea analyses. So I create my own database looks like this : df_db <- read.csv('pathway_ecnumber.csv',sep=",") df_db path:map00010...pathways, stats, minSize, maxSize, gseaParam, : There are duplicate gene names, fgsea may produce unexpected results. The second warning I try to resolve with this line but it is not working : df_database

R fgsea

updated 2.4 years ago • julie.hardy

S2N metric implemented in GSEA (I just wrote a function to perform this for me and feed it into fgsea). I got everything to work but I'm trying to ensure what I see is actually real. Please see the image below as a representative

fgsea gsea sc-rnaseq

updated 5.2 years ago • atakanekiz

Part of the input for Gene Set Enrichment Analysis with [fgseaMultilevel](https://rdrr.io/bioc/fgsea/man/fgseaMultilevel.html) is a list of GO terms and genes assigned to it. E.g.: ``` library(fgsea) data(examplePathways) examplePathways...all of the ancestor terms. This means that data retrieved from biomart is not immediately usable for `fgsea`. Here's an example: At first impression…

biomaRt GO ensembldb fgsea

updated 11 months ago • dario.beraldi

I try to run the example of fgsea package with R version 4.0.2 : ```r data(examplePathways) data(exampleRanks) typeof(examplePathways) fgseaRes <- fgsea...I try to run the example of fgsea package with R version 4.0.2 : ```r data(examplePathways) data(exampleRanks) typeof(examplePathways) fgseaRes <- fgsea(pathways = examplePathways, stats = example…

fgsea fgse

updated 2.4 years ago • julie.hardy

Recently, I have seen a post about `fgsea` for gene set enrichment analysis. In this [DESeq results to pathways in 60 Seconds with the fgsea package][1]. In this post...How to get the t-statistic using edgeR package? [1]: https://stephenturner.github.io/deseq-to-fgsea

r edger t-statistic fgsea gsea

updated 4.4 years ago • Biologist

implement functions for a Gene Set (Enrichment) Analysis, some of them are limma, gsar, gsva, piano, fgsea, pgsea. However I couldn't find an agreement for those tests which accept any statistic as input: `` fgsea ``, `` runGSA ``, `` geneSetTest

gsea concept gsa

updated 6.6 years ago • Lluís Revilla Sancho

finish computation. When I manually stop it I get the error message: <pre> Warning message: In fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize, : There are duplicate gene names, fgsea may produce

reactomepa reactome gsea fgsea

updated 5.3 years ago • martin.busch

nbsp; I tried to install "Chipseeker" on Linux CentOS7. but the problem occured. it said that "fgsea, DOSE, chipseeker had non-zero status exit".   is the package, Chipseeker undecent on Linux

Bioconduct or Chipseeker CentOS7 Linux installation

updated 6.9 years ago • spsp9987

Hi Is it possible to run ViSEAGO with results obtained by the ``fora`` function of the fgsea package? More specifically, I want to cluster the significant pathways from ```fora``` by semantic similarity. My ultimate

ViSEAGO

updated 2.5 years ago • tim.meese

my differential gene expression analysis. If I understand it correctly, `clusterProfiler::GSEA` uses `fgsea` under the hood to estimate significance levels and for that, it permutates the **gene labels**. However, if I remember correctly

clusterProfiler GSEA fgsea

updated 9 months ago • nhaus

We do not recommend using nPerm parameter incurrent and future releases > 2: In fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize, : > You are trying to run fgseaSimple. It is recommended...use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm > argument in the fgsea function call

clusterprofiler

updated 3.2 years ago • sunnykevin97

Hi everyone; just want to double check my understanding of leading Edges in fgsea; according to FAQ of original gsea > "For a positive ES (such as the one shown here), the leading edge > subset is the set...Hi everyone; just want to double check my understanding of leading Edges in fgsea; according to FAQ of original gsea > "For a positive ES (such as the one shown…

fgsea

updated 3.2 years ago • kavator

changes generated by apeglm as the test statistic for gene set enrichment analyses when running the fgsea package. I have seen a paper that suggests the absolute value of Signal-To-Noise is a better metric than LFC: https://bmcbioinformatics.biomedcentral.com

apeglm fgsea Signal-To-Noise Ratio

updated 4.4 years ago • coulsonr

But it comes out the error. Thank you in advance for great help! Best, Yue > library(fgsea) > library(tidyverse) > library(data.table) > library(ggplot2) > setwd("/media/hp/04c65089-71ff-4b33-9a30-c21b8c77eda2...gt; pathways.kegg<- gmtPathways("c2.cp.kegg.v7.2.symbols.gmt") > fgseaRes_kegg<- fgsea(pathways = pa…

fgsea

updated 2.6 years ago • yueli7

and GSEA. Then we paste the results into a file that we can save as a CSV file ```{r} library(fgsea) library(enrichR) library(clusterProfiler) library(dplyr) genes <- data.frame(d$log2FoldChange, d$symbol) names(genes...lt;- d$symbol genes <- genes %>% dplyr::arrange(desc(d.log2FoldChange)) library(fgsea) library(enrichR) library(clusterProfiler) em <- enricher(gene…

clusterProfiler

updated 9 months ago • Rob

I have been using voom+limma+sva to analyse my RNA-Seq data of leukaemia. After some clustering analysis and prior knowledge to the data set, I now am trying to compare some of the samples in a group with the remaining data set. I used fgseaMultilevel() from fgsea package and did a pre-ranked GSEA using log(fold change) as the ranking matrix. However, as it is RNA-Seq data, I actually want...t…

limma deseq2 seqgsea sva deseq

updated 4.2 years ago • kentfung

I'm interested in this because, from what I have read, the stat column is useful for GSEA analysis (fGSEA package) and from what I have found and is posted in the vignette I get the impression it is best to use shrinkage for downstream

deseq2 stat lfcshrink

updated 3.5 years ago • divercory

2 Homo sapiens: Interleukin-6 signaling 1059683</code> As this behavior breaks build of my package (fgsea) and I need to fix it, I wonder is this transition final? If yes, may be it's better to remove organism specific prefix whatsoever

reactome.db fgsea

updated 6.4 years ago • assaron

nbsp;  verbose = TRUE,      seed = FALSE,      by = "fgsea") " \#\# <pre> preparing geneSet collections... --> Expected input gene ID: 94094,223650,17926,12831,29875,68178 Error in check_gene_id

GSEA clusterProfiler

updated 5.8 years ago • giuseppe0525

organism in the form of `.gmt` file, which is very useful for gene set enrichment tools like `fgsea`. Coming back to use the code a year later, I discovered that `keggGet` command started to fail when trying to retrieve modules

keggrest software error pathways modules kegg

updated 3.4 years ago • predeus

Hi, I am running gene set enrichment analysis on R using the `fgsea` package and plotting the results using `ggplot`. The main code for plotting the results is as follows: ``` ggplot(fgseaRes_sig

ggplot

updated 21 months ago • nattzy94

nbsp;verbose = TRUE,       seed = FALSE,       by = "fgsea")_   3. However, I run the gseaplot() function with another gsearesults object derived from gsekegg() function..._data = FALSE,         seed = FALSE,      &nbs…

gsea clusterprofiler

updated 5.8 years ago • giuseppe0525

Dear Bioconductor admin, I am working on data analysis for microarray data, but I could not install into my R studio, Could you please help to solve my issue that How to install "maEndToEnd" into R studio in my Macbook? Thank you very much Here is the problem report from my screen: ``` > library(devtools) > library(remotes) > remotes::install_github("b-klaus/…

microarray maEndToEnd

updated 4.0 years ago • Jack

pvalueCutoff = 0.05, verbose = TRUE, OrgDb = organism, by = "fgsea", pAdjustMethod = "none") require(DOSE) library(enrichplot) library(DOSE) edo2dot <- gseDO(sorted_dfx) #barplot(gse, showCategory

clusterProfiler enrichplot clusterpro doseR dose

updated 14 months ago • rama

71), bit(v.1.1-14), Formula(v.1.2-3), AnnotationForge(v.1.22.2), htmlwidgets(v.1.3), httr(v.1.3.1), fgsea(v.1.6.0), acepack(v.1.4.1), pkgconfig(v.2.0.2), XML(v.3.98-1.16), farver(v.1.0), nnet(v.7.3-12), locfit(v.1.5-9.1), labeling(v.0.3

diffbind

updated 4.7 years ago • avantika6194

nbsp;   RSQLite\_1.0.0        stringi\_1.1.2        fgsea\_1.0.2          GO.db\_3.4.0          \[36\] scales\_0.4.1         stats4\_3.3.2

clusterprofiler

updated 6.8 years ago • Marcus

packages/3.4/extra/bin/windows/contrib/3.4/PACKAGES' Old packages: 'AnnotationHub', 'curl', 'fgsea', 'GenomicAlignments', 'GenomicRanges', 'GOSemSim', 'IRanges', 'limma', 'Rsamtools', 'S4Vectors',   'VariantAnnotation', 'XVector

deseq2 DESeqDataSetFromMatrix

updated 6.2 years ago • zxy5139

nbsp;    rvcheck\_0.0.9       gridExtra\_2.3 \[19\] fgsea\_1.4.0         stringr\_1.2.0       tidyselect\_0.2.3 \[22\] autoinst

clusterProfiler GO GO enrichment genesetenrichment

updated 5.8 years ago • Huang, Lei [BSD] - CRI

rgl) library(tradeSeq) library(bioc2020trajectories) library(pheatmap) library(msigdbr) library(fgsea) library(ggplot2);library(gridExtra) library(condiments) library(clusterProfiler) epi <- readRDS("fromAvital/Epi_sub_clusters.rds

tradeSeq slingshot

updated 14 months ago • manduchi

nbsp;        genefilter\_1.60.0      fgsea\_1.4.0            reshape2\_1.4.2         &nbsp

clusterProfiler

updated 5.8 years ago • GFM

nbsp;     munsell\_0.4.3          fgsea\_1.2.1           \[25\] compiler\_3.4.0         KEGGREST

pathview

updated 6.3 years ago • joseph

nbsp;        \[21\] RColorBrewer\_1.1-2          fgsea\_1.6.0                 Rcpp\_0.12.18                forcats\_0.3.0

deseq2 phyloseq

updated 5.0 years ago • eoin

_1.46.2           loaded via a namespace (and not attached):   \[1\] fgsea\_1.6.0           colorspace\_1.3-2      ggridges\_0.5.0        rprojroot\_1.3

flowworkspace parseWorkspace parseWorkspace

updated 5.0 years ago • vonskopnik

2021-01-25 [1] CRAN (R 4.2.0) fastmatch 1.1-3 2021-07-23 [1] CRAN (R 4.2.0) fgsea * 1.22.0 2022-04-26 [1] Bioconductor filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.0) fitdistrplus 1.1-8 2022-03-10 [1] CRAN (R 4.2.0) fs

clusterProfiler

updated 14 months ago • Y.K

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

annotationforge

updated 5.2 years ago • lukeholman

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

annotationforge GSEA clusterprofiler GO annotation

updated 6.1 years ago • cabezasdelafuented

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…

clusterprofiler

updated 5.9 years ago • akleens1

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…

download fgsea

updated 5 weeks ago • luca.s