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Questions tagged [gsea]

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I am getting a parsing error when uploading .chip file to GSEA software

I get the following error when I try to load a .chip file to GSEA software. What is the problem? ...
ham123's user avatar
  • 51
2 votes
0 answers

GSEA vs GSVA: Pros and cons of each method

Trying to understand when GSEA is more appropriate than GSVA and vice versa. I have seen cases when running GSEA and GSVA on the same task - compare enrichment of a geneset between two groups - gives ...
Tomas Bencomo's user avatar
1 vote
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Trying to plot the results of GSEA in python

I'm having some major chaos with the output table generated and then passing that to my plot function. New to this (1st time), could somebody review this piece of code and suggest some corrections. I ...
aleksk31's user avatar
1 vote
0 answers

GSEA results plot interpretation

I need to plot the results of a GSEA analysis we performed on scRNA data. I am stumbling upon various possibilities for this and sometimes I am struggling a bit to understand how to interpret it. My ...
edo988811's user avatar
1 vote
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enrichment of DE genes within wide regions not pathways, hypergeometric test or GSEA?

I haven't found any relevant posts, so here is my question (it's more a question on statistics I believe): I have the deseq2 output of DE genes( around 25000 genes) , and among them 1000 are ...
dew's user avatar
  • 11
1 vote
0 answers

Correlate ssGSEA score with Seurat's scaled expression data

I want to check the correlation between the expression of a given "test_gene"* in each cluster within a scRNA-seq database with the expression of a signature (i.e., gene sets whose ...
samge's user avatar
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1 vote
0 answers

GSEA. Subsetting Gene Ontology, Biological Processes, by gene set families of interest

I have run GSEA - on Gene Ontology , Biological Processes (GO and BP hereafter) - on some Mouse bulk RNA-seq data, and am currently in the process of going through the results. To do this, I have used ...
h3ab74's user avatar
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1 vote
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Question about enrichment score (ES) and NES from GSEA

I have two results from two separate GSEA runs (2 different inputs / samples with same gene sets), and i want to know which sample has the most enrichment about specific pathway (gene set). I want to ...
yepp's user avatar
  • 11
0 votes
1 answer

Error in Load Data in GSEA 4.3.3

I've made my files for a GSEA ANALYSIS, but the software gives me this error: ...
user20358's user avatar
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Error in GSEA expresion data set file

I'm want to perform an GSEA of some RNA-seq data but when I upload the expression data set file this problem appears but I don't know how to solve it. Thanks for your help. Pol Error Details ...
Pol's user avatar
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How can I use QIAGEN Ingenuity Pathway Analysis (IPA) on proteomics data associated with an outcome?

I am trying to do pathway analysis on a set of proteins associated with several outcomes (one is continuous, the others four are binary). I have run independent associations between the proteomics ...
womy's user avatar
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Run gmt format download from GSEA

I built the matrix as the gmt example in but It still has errors when I try to run it. When I try the gene set from
Nerea Herrera's user avatar
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Making a list of lists in R

I have a data frame columns are pathways and genes are rows Like ...
Zizogolu's user avatar
  • 2,160