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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 ...
  • 4,622
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 ...
  • 3,221
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 ...
  • 463
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 ...
  • 4,622
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 ...
  • 806
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 ...
  • 12k
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. ...
  • 621
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 ...
  • 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 ...
  • 4,622
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 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 ...
  • 12k
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: ...
  • 19.3k
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,...
  • 873
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&...
  • 4,622
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 ...
  • 4,622
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 ...
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.
  • 503
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
1 vote

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

I think the typical way to do this would be to identify a small number of marker genes whose presence and absence is specific for that cell type.
  • 1,722
1 vote
Accepted

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

Use removeBatchEffects from limma. The input counts should be on log scale, so vst and ...
1 vote

#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.
  • 21
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.
1 vote

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

The noise is comming from the subset.mask, which is created above in a loop with the number of permutations. ...
  • 4,622
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 ...
  • 12k
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 ...
  • 2,099
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 ...
  • 4,622
1 vote

How to convert data in gmt format to dataframe?

You can use GSA.read.gmt function from GSA package. The following code can be used to convert the file to a dataframe. Just ignore the warnings. Original_response ...

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