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 ...
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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 ...
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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 ...
- 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 ...
- 4,693
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 ...
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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 ...
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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.
...
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3
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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 ...
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3
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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 ...
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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
2
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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 ...
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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:
...
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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,...
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2
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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.
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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&...
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2
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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 ...
- 4,693
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 ...
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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
2
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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 ...
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2
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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" ...
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1
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#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.
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1
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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.
- 535
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 ...
- 13.8k
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 ...
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 ...
- 2,169
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 ...
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1
vote
Can I use GSEA to look for enrichment in data that is grouped into sets but are not necessarily genes?
Yes, if you have a ranked list, you can use GSEA to calculate the enrichment of the strains along the ranked list.
Note that hypergeometric test is for count data, so you would test if there are ...
- 4,693
1
vote
I get the following error when using the GSEA software 'Enrichment Map Visualization' tool using the Cytoscape 3.7.1 application
This is a tough one, because the only relevant lines from your GSEA debug log were these two:
...
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