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8 votes
1 answer
641 views

Comparison of gene set enrichment statistics

I am performing a gene set enrichment analysis to determine if particular gene sets are coherently up- or down-regulated. I have seen several statistics for computing a p-value of GSEA-style ...
Nuclear Hoagie's user avatar
6 votes
2 answers
296 views

Clarification on Gene Enrichment

When I run a GSEA analysis on two conditions from the same RNaseq (negative control PBS injection VS positive control CpG injection) from the same dataset/same gene list, I get results that look ...
julianstanley's user avatar
5 votes
3 answers
9k views

Script to allow gene set enrichment analysis of 10x genomics data in R

I have 10x single cell RNA seq data. Which R package is best suited for analysis of the 10x data matrix. What is the script to prepare the data for downstream GSEA analysis. I have already processed ...
Jay's user avatar
  • 51
5 votes
3 answers
287 views

How to adapt the fgseaL function to perform rapidGSEA computation of gene ranks across 9 different phenotype labels?

I wish to adapt the r language function fgseaL, https://github.com/ctlab/fgsea , to perform rapidGSEA, https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1244-x , computation of ...
Frank's user avatar
  • 191
5 votes
1 answer
372 views

are GSEA and other geneset enrichment analysis supposed to yield extremely different results between them?

I have recently ran in R four geneset enrichment analysis in the same database (TCGA:breast cancer) comparing two intrinsic subtypes. The methods I used were: MIGSA, that imports mGSZ package and ...
Darío Rocha's user avatar
4 votes
1 answer
578 views

Gene Ranking - signal to noise ratio used in GSEA-P algorithm?

I'm looking at Broad Institute's orignal GSEA-P algorithm R script which I downloaded here: http://software.broadinstitute.org/gsea/downloads.jsp. I'm trying to adapt their GSEA.1.0.R script to ...
lrthistlethwaite's user avatar
3 votes
2 answers
79 views

Is there anything similar to GSEA for locus-based (instead of of gene-based) data?

As the question states, I am interested in an analysis similar to Gene Set Enrichment Analysis (ranked gene sets) but focused on locus-level data instead of genes. To explain in greater detail: I ...
Reilstein's user avatar
  • 367
3 votes
1 answer
311 views

Why are asymmetric distributions an issue for GSEA?

I'm reading Subramanian et. al's (2005) original GSEA paper. In the paper, the authors mention the following: We noticed that the use of weighted steps could cause the distribution of observed ES ...
An Ignorant Wanderer's user avatar
3 votes
0 answers
571 views

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
2 answers
43 views

How to perform meaningful Gene set erichment analysis or otherwise find broader themes/functions in different cell populations?

(For context: I'm somewhat new to bioinformatic analyses but am mostly comfortable with R) I have identified transcriptomically and morphologically different cancer cell populations within a patient (...
immunoLogical's user avatar
2 votes
2 answers
86 views

Is the potential skewing of FDR and ranking of gene set analysis with gene sets with hierarchical structure a concern?

When performing GSEA and many other gene set analysis, when gene sets with hierarchy such as KEGG collection or Reactome collection, the FDR could be skewed sometimes, and the ranking of gene sets by ...
Kento's user avatar
  • 67
2 votes
1 answer
67 views

RNAseq small sample size in control group

I am doing an RNAseq experiment with affected (n=6) and control groups (n=6) in cow. However it turned out that 4 of my control samples have very low quality so I have to discard them. My problem is ...
Balint Biro's user avatar
2 votes
1 answer
2k views

GSEA- parsing error for .cls file

I am creating a .cls file for my GSEA analysis and see the below error. Can anyone suggest a solution? I create the file using TeXworks. The file looks like this: ...
Son nguyen's user avatar
2 votes
1 answer
3k views

#1 Parsing trouble java.lang.NumberFormatException in GSEA 4.2.1

I am getting the following error message when I tried to load .TXT data file to GSEA 4.2.1. I tried different way to change the file name as .GCT but not working. Any suggestion? Many thanks. Full ...
Hong's user avatar
  • 41
2 votes
1 answer
93 views

GSEA: Computing an Enrichment Score (as described in the original paper)

The following paragraph comes from the GSEA paper that explains how to obtain an enrichment score for a gene set. Note that the enrichment score is computed up to a position i in L. There are 2 things ...
An Ignorant Wanderer's user avatar
2 votes
2 answers
2k views

Interpreting this plot from GSEA

I have RNA-seq for two groups of patients: Responders to chemotherapy (n=9) versus ...
Zizogolu's user avatar
  • 2,160
2 votes
1 answer
652 views

I get the following error when using the GSEA software 'Enrichment Map Visualization' tool using the Cytoscape 3.7.1 application

I am trying to visualize a GSEA analysis I conducted using the Broad Institute's GSEA Enrichment Map Visualization, however I get the following error and am not sure what the issue is: any help would ...
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
2 answers
1k views

Ranking metric in GSEA

I am using fgsea in r to calculate and plot a bunch of GSEA graphs. My question is whether it is acceptable to use the Wald statistic from DeSeq2 to rank the gene list? I have seen in the GSEA ...
Jack Henry's user avatar
1 vote
2 answers
800 views

GSEA - Gene Set Enrichment Analysis - in R studio

I have been trying to conduct a classic GSEA using the broad institute software and can not figure out how to compile it in R for the life of me. I am aware that there exists other packages in R that ...
h3ab74's user avatar
  • 846
1 vote
3 answers
6k views

How to convert data in gmt format to dataframe?

I downloaded c5: gene ontology gene sets file from http://software.broadinstitute.org/gsea/downloads.jsp I opened the "c5.all.v6.2.symbols.gmt" file in csv format and It looks like below: I want to ...
beginner's user avatar
  • 631
1 vote
1 answer
75 views

Retrieving gene matrix from internet in GSEA desktop

This error appeared to me, and I have the program connected to the internet. I already installed java 8, but it still doesn't get me the gene set databases.
Sofia's user avatar
  • 351
1 vote
1 answer
54 views

Gene Set Comparison Without Expression Data

I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated ...
Eliza R's user avatar
  • 11
1 vote
1 answer
43 views

How can to validate the presence of a certain type of cells in a single cell dataset?

I have a single cell dataset which I consider to be a reference , let say, for an human organ, I have identified some new clusters that correspond to cell types. I also have WGCNA modules that ...
MrPapouille's user avatar
1 vote
1 answer
141 views

Can I Incorporate svaseq() into GSEA/GSVA analysis?

I understand GSEA/GSVA can take microarray-like expression matrix such as the output of voom() or vst(). However, I have a question on how we can also use svaseq() variables, correct the output from ...
Kento's user avatar
  • 67
1 vote
1 answer
888 views

How to run GSEA analysis on R studio using DEG file list generated from scRNAseq analysis

I want to draw the standard plot of GSEA on Rstudio. I have a data frame that consists of a list of DEGs as below. Actually, I put the DEG list directly to PANTHER that resulted in the GO or pathway ...
raiora's user avatar
  • 77
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
  • 846
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
246 views

Is there an established method for comparing expression of groups of genes (gene sets)?

I have a figure in a paper where I show the log2(fold-change) (obtained with DESeq2) between two groups (based on genotype) for genes within a specific hallmark gene set, and a reviewer is asking ...
Reilstein's user avatar
  • 367
0 votes
1 answer
154 views

Running GSEA or comparable analysis with multiple variable interaction?

I am working with an RNA-seq dataset generated from a complex experimental design. Our main question is focused on the interaction between two variables, one (INJ) with two conditions (L,S) and the ...
jfaberha's user avatar
0 votes
1 answer
57 views

Pathway Enrichment Analysis for one specific pathway?

I have a gene set containing a set of 1500 genes in which I did differential gene expression using limma voom pipeline. After this step I wanted to analyze a specific set of pathways the metabolism ...
Manuel Srgio Sokolov Ravasquei's user avatar
0 votes
1 answer
80 views

GSEA enrichr with 10x genomics differential_expression ranks

I am attempting to use GSEA enrichr with 10x genomics differential_expression rankings. Reading what people seem to be doing with GSEA, there seems to be a pre-/post-singlecell gene expression ...
719016's user avatar
  • 2,324
0 votes
2 answers
671 views

GSEA preranked different results opposing phenotypes

I am running an analysis of two phenotypes: mutant and control. I have a statistic used to rank the different genes, and the ranking is exactly the opposite between mutant and control. Moreover, there ...
gc5's user avatar
  • 1,813
0 votes
1 answer
26 views

Can I use GSEA to look for enrichment in data that is grouped into sets but are not necessarily genes?

I have yeast growth data in various experimental conditions that are classified by the strain type. Can I use the GSEA tool from the Broad Institute to test for enrichment of specific groups of ...
ham123's user avatar
  • 51
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
  • 1
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
  • 23
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
-1 votes
2 answers
612 views

How to do pathway analysis after scanpy for single cell data after DE analysis?

I have done DE analysis using SCANpy on my single cell data and I have compared each cluster versus all the other clusters. One cluster seems particularly interesting so I wanted to do pathway ...
pythonbeginner's user avatar