8 votes
Accepted

Clarification on Gene Enrichment

If you compare A vs B the genes's fold change will have the opposite sign to B vs A. So will be the gene set up or down-regulated depending on the comparison to take. The gene set test analyze if a ...
llrs's user avatar
  • 4,703
5 votes

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

Seruat will give you a list of genes which it thinks are upregulated in a particular cluster. Look at the functions that talk about marker genes - these functions basically do a DE analysis of the ...
Ian Sudbery's user avatar
  • 3,311
5 votes

Clarification on Gene Enrichment

While I'm not familiar with GSEA software in particular, I believe your problem is that it only tests for upregulated gene sets. Notice: 866/4408 gene sets are upregulated 3542/4408 gene ...
juod's user avatar
  • 473
4 votes

Comparison of gene set enrichment statistics

I assume that you are talking about the implementation of these methods in the limma package. Otherwise this answer does not apply. I think that your questions can be answered with some simulations ...
llrs's user avatar
  • 4,703
4 votes

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

Additionally there are plenty of tools to summarize long lists of GO terms by removing redundancy (which seems to be your concern), such as REVIGO (web) or rrvgo (R+Bioconductor). Disclaimer: I'm the ...
ssayols's user avatar
  • 141
3 votes

Ranking metric in GSEA

If using DESeq2 with GSEA, I'd recommend ranking by shrunk log2FC values. It'd also be worth considering ranking positive and negative associations separately, because the standard GSEA algorithm ...
gringer's user avatar
  • 14.1k
3 votes

GSEA - Gene Set Enrichment Analysis - in R studio

I have answered my own question however, it is specific to windows users.. If you get the same error from the cmd as I did, you must manually put in environment ...
h3ab74's user avatar
  • 836
3 votes

How to convert data in gmt format to dataframe?

Ok. Answering my own question. I did this way. And I got the output I want. ...
beginner's user avatar
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3 votes

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

I finally found another answer to my question. Please read this great article in May 12 2017 BioMed Central (BMC) Bioinformatics article titled Ranking metrics in gene set enrichment analysis: do they ...
Frank's user avatar
  • 191
3 votes

GSEA- parsing error for .cls file

You seem to have forgotten the space after the #. It should be as in here (Just for future readers know where to find the specs). Also it should be a single line (Maybe this error was introduced while ...
llrs's user avatar
  • 4,703
3 votes

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

It is totally acceptable in your main figure to display only a selected part of your GO term, as long as the reader is aware of this action (e.g., by including a legend specifying "selected ...
RomainL.'s user avatar
  • 145
2 votes
Accepted

Retrieving gene matrix from internet in GSEA desktop

Have you checked firewall settings on your laptop? See Firewall / FTP connection issues at: GSEA wiki - known issues
Kasper Thystrup Karstensen's user avatar
2 votes

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

I tinkered with a program GSEA-SNP quite a few years back, which claims that it does a similar ranking procedure with SNPs. It carries out its procedure by first linking SNPs with genes, then running ...
gringer's user avatar
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2 votes
Accepted

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

You rank the fit coefficient rather than the original score matrix. So, given a score matrix, D: ...
Devon Ryan's user avatar
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2 votes

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

There is no purpose-built R package to perform gene set enrichment analysis on single-cell data but there does not need to be. You should be able to tools developed for bulk-RNA-Seq or microarray data,...
Tom Kelly's user avatar
  • 873
2 votes

GSEA - Gene Set Enrichment Analysis - in R studio

Are you calling java with sufficient memory? Try increasing -Xmx2G to -Xmx8G, provided your PC has 8 GB RAM.
Pallie's user avatar
  • 707
2 votes
Accepted

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

Each of these methods do something different, so it is reasonable to expect different results. The bottom line is that there isn't a single question you can ask when you do an "enrichment test&...
llrs's user avatar
  • 4,703
2 votes
Accepted

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

You could apply the GSVA transformation to later compare them. You would need to give a step back and start from the expression values not log2FC, but I think it would be better than using the log2FC ...
llrs's user avatar
  • 4,703
2 votes
Accepted

Running GSEA or comparable analysis with multiple variable interaction?

I'm not sure I understand "I would like to run GSEA or a similar analysis to find WGCNCA clusters that differ based on the interaction between the two main variables". I would run an ...
Peter Langfelder's user avatar
2 votes

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

I just figured out the error. My .TXT was not correctly formated, following the instruction from their manual under .TXT format worked.
Hong's user avatar
  • 41
2 votes
Accepted

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

Actually I believe I get it now. i is not a constant. We vary it from i=1 to N and consider the i for which $P_{hit} - P_{miss}$ is largest in magnitude
An Ignorant Wanderer's user avatar
2 votes

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

Statisticians might kill me for it but I've always filtered long and redundant geneset lists to only contain what remotely makes biological sense in my setup. If I am investigating leukocyte ...
ATpoint's user avatar
  • 1,237
2 votes
Accepted

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

This is actually a known problem in the correction of nominal p-values in over-representation analyses that use the Gene Ontology categories (commonly but misleadingly called "GO enrichment" ...
gdagstn's user avatar
  • 131
1 vote

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

I'd probably just use fgsea. Your code won't have to change much, it also just uses a ranked list.
Jared Andrews's user avatar
1 vote
Accepted

Interpreting this plot from GSEA

A gene set enrichment analysis (GSEA) tests for enrichment of a gene set within a ranked list of genes. The primary outcome of the analysis is enrichment or no enrichment. Gene sets frequently include ...
gringer's user avatar
  • 14.1k
1 vote

Interpreting this plot from GSEA

In Deseq2, it depends on contrast eg. if your contrast <- c("Condition", firstC, SecondC) is then -ve is ...
Amarinder Singh Thind's user avatar
1 vote

GSEA enrichr with 10x genomics differential_expression ranks

You should be using the most positive fold changes, not the most negative. The positive ones are the ones that are most highly expressed in your cluster of interest. You probably want to use less than ...
burger's user avatar
  • 2,179
1 vote

GSEA preranked different results opposing phenotypes

There are two things that I notice from these plots that are unusual for GSEA analyses that people do: The zero cross is at the extreme end of the plot, meaning that all selected genes have a ...
gringer's user avatar
  • 14.1k

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