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Questions tagged [gsea]

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3 votes
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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
237 views

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
0 answers
21 views

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
50 views

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
0 answers
38 views

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
107 views

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
  • 11
1 vote
0 answers
48 views

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
0 answers
324 views

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
13 views

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
0 votes
0 answers
24 views

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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0 votes
0 answers
37 views

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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0 votes
0 answers
43 views

Run gmt format download from GSEA

I built the matrix as the gmt example in https://docs.gsea-msigdb.org/#GSEA/Data_Formats/ but It still has errors when I try to run it. When I try the gene set from https://www.gsea-msigdb.org/gsea/...
Nerea Herrera's user avatar
0 votes
0 answers
49 views

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