Question: GSEA Leading edge analysis error
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gravatar for sandKings
13 months ago by
sandKings10
sandKings10 wrote:

hi all!

I'm trying to run a leading edge analysis on my RNASeq data.

Hi everyone!

I'm trying to run a leading edge analysis on my RNASeq data using GSEA

I first create a ranked gene set file and run GSEA Prerank analysis.

I use the GMT file from http://download.baderlab.org/EM_Genesets/current_release/Mouse/symbol/Mouse_GOBP_AllPathways_no_GO_iea_February_01_2018_symbol.gmt

Once I run the GSEA Preranked analysis, I try running the Leading edge analysis and run into this error https://imgur.com/a/zX3YI

It says:

---- Stack Trace ---- of exceptions: 1 ------In GeneSetMatrix: gene_sets.gmt no GeneSet found with name: TRANSMEMBRANE RECEPTOR PROTEIN SERINE\THREONINE KINASE SIGNALING PATHWAY%GOBP%GO:0007178

Searching the gene_sets.gmt file in notepad++ for the "missing" geneset shows that the and I find it to be present:

The line looks like this:

TRANSMEMBRANE RECEPTOR PROTEIN SERINE/THREONINE KINASE SIGNALING PATHWAY%GOBP%GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway Ddx5 Sub1 Zyx Bmpr1b Chrd Trps1 Tob1 Scx Inha Nup93 Ptprk Tmem100 Id1 Trf Mir23a Ccl2 Zcchc18 Pml Dand5 Vim Zfyve9 Map3k7 Acvr2b Hfe2 Parp1 Eid2 Acvr1b Itgb5 Lrp4 Map3k1 Bmp6 Acvr1c Bmp5 Mtmr4 Bmp3 Dcp1a Tab1 Akap2 Col1a2 Col3a1 Ppm1l Magi2 Rgmb Twsg1 Src Rbm14 Atoh8 Nceh1 Tgfb3 Tgfbr1 Nlk Creb1 Usp15 Tgfb2 Smad6 Amhr2 Inhba Eng Sptbn1 Fermt2 Tgfbr3 Dusp22 Tgfbr2 Tgfb1 Ecsit Jun Gdf10 Rnf111 Pxn Smad1 Gdf15 Smad2 Btbd11 Smad5 Smad3 Smad4 Pdcd4 Fut8 Cldn5 Egr1 Mapk3 Adam9 Trp53 Acvr1 Fos Tgfb1i1 Hfe Stoml1 4632428N05Rik Bmpr2 Smad7 Sirt1 Lnpep Inhbb Slc33a1 Bmp8a Bmp8b Smurf1 Msx2 Usp9x Bmp4 Cited2 Bmp7 Fam83g Ptk2 Myd88 Bmpr1a Skil Mapk14 Runx2 Akap7 Megf8 Smurf2 Gdf5 Acvrl1 Rgma Meg3 Dlx5 Gdf9 Hpgd Itgb1 Fst Ski Bmp15 Tgif1 Ror2 Tgif2 Nog Zfp128 Acvr2a Ltbp3 Ltbp1 Ltbp4 Gdf11 Stub1 Hipk2 Bambi Fkbp1a Gcnt2 Lefty1 Msx1 Lef1 Cited1 Cdh5 Arrb2 Bmp2 Hexa Smad9

So, if it's present in the gene_sets.gmt, why am I getting this error?

Could someone please help me troubleshoot this?

Thanks!

gsea rnaseq • 585 views
ADD COMMENTlink written 13 months ago by sandKings10
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