Fgsea not all stats values are finite numbers
WebA tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. WebSep 19, 2024 · I am trying to generate a kegg pathway based on rna sequencing data. When I get to the following step however (see attached image) I continuously get the following error: "not all stats values are finite numbers" However, when my friend uses my data and repeats the codes on her R she does not get the error?
Fgsea not all stats values are finite numbers
Did you know?
WebFgsea The package implements an algorithm for fast gene set enrichment Summary Functions calcGseaStat () Calculates GSEA statistics for a given query gene set calcGseaStatBatchCpp () Calculates GSEA statistic valus for all gene sets in selectedStats list. collapsePathways () Collapse list of enriched pathways to independent ones. … http://rvdsd.top/2024/09/10/BioTools/fgsea/
WebJan 20, 2024 · Star 755 New issue gseGO Error in preparePathwaysAndStats (pathways, stats, minSize, maxSize, gseaParam, : Not all stats values are finite numbers #422 … WebNov 8, 2024 · fgseaMultilevel ( pathways, stats, sampleSize = 101, minSize = 1, maxSize = Inf, eps = 1e-10, scoreType = c ("std", "pos", "neg"), nproc = 0, gseaParam = 1, BPPARAM = NULL, nPermSimple = 1000, absEps = NULL ) Arguments Value A table with GSEA results. Each row corresponds to a tested pathway. The columns are the following
WebAug 27, 2024 · That means that the statistic values are not symmetric and the probability of having positive (or negative) enrichment score is far from 0.5. In such cases it can be very hard to estimate P-values. It can be a sign of gene expression data not being properly normalized before differential expression. WebBioconductor version: Release (3.16) The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Author: Gennady Korotkevich [aut], Vladimir Sukhov [aut ...
Webfgsea/R/plot.R Go to file Cannot retrieve contributors at this time 281 lines (248 sloc) 10.7 KB Raw Blame cowplotText <- function (text, style) { ggdraw () + do.call …
Webfgsea is an R-package for fast preranked gene set enrichment analysis (GSEA). This package allows to quickly and accurately calculate arbitrarily low GSEA P-values for a … binding of isaac wiki tainted judasWebYou need: t.stat <- sign (qlf$table$logFC) * sqrt (qlf$table$F) z <- zscoreT (t.stat, df=qlf$df.total) The z-statistic should be input to fgsea rather than the t-statistic because the t-statistics are not all on the same df. You won't be surprised though that I feel that camera would be better. cystoscopy laser lithotripsycystoscopy litholapaxy procedureWebJun 20, 2024 · Warning message: In fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize, : There are ties in the preranked stats (11.03 % of the … cystoscopy length of timeWebSep 10, 2024 · fgsea这个包用于做GSEA分析，先来看一下使用这个包做的图，如下所示： 现在简单解释一下这个图形： x轴——排序后的基因列表 L 位置对应的坐标，也就是我 … binding of isaac worst itemsWebFeb 1, 2024 · Using the exact algorithm as a reference we show that FGSEA is able to routinely estimate P-values up to 10 −100 with a small and predictable estimation error. We systematically evaluate FGSEA on a collection of 605 datasets and show that FGSEA recovers much more statistically significant pathways compared to other implementations. cystoscopy is surgeryWebfgsea is an R-package for fast preranked gene set enrichment analysis (GSEA). This package allows to quickly and accurately calculate arbitrarily low GSEA P-values for a collection of gene sets. P-value estimation is based on an adaptive multi-level split Monte-Carlo scheme. suppressPackageStartupMessages ( library ( fgsea)) cystoscopy left ureteral stent placement