Question: GSEA preranking metric for RNA Seq
0
gravatar for bipin
3.0 years ago by
bipin20
bipin20 wrote:

I came across multiple posts regarding the pre-ranking metric for GSEA when using RNA seq data. However, there doesn't seem to be a consensus.

Some of the metrics I came across are:-

  • sign of log fold change * -log10(p-value[not adjusted p-val])
  • logfc shrink values from DESeq2
  • Inbuilt signal2noise from GSEA. However, this cannot be used in case of <3 replicates.

What metric do you use for ranking the genes or you know is widely used?

gsea rna-seq deseq2 • 3.8k views
ADD COMMENTlink modified 3.0 years ago by Kevin Blighe70k • written 3.0 years ago by bipin20
6
gravatar for Kevin Blighe
3.0 years ago by
Kevin Blighe70k
Republic of Ireland
Kevin Blighe70k wrote:

Edit 31st July, 2019: I gave my original answer (below) assuming that you were referring to the general process of gene enrichment (or 'gene-set enrichment analysis'), and not that you were referring to GSEA, the Broad Institute's PROGRAM that hijacked the term GSEA

GSEA (the Broad Institute program) permits a ranked list of genes, as does topGO (R), fGSEA (see my comment below), and other enrichment programs - there are too many programs.

---------------------------------------------

It makes sense that there is no consensus, as there are countless ways to do this. My own recommendation would be to:

  1. Set an adjusted P value cut-off
  2. Rank genes based on absolute log (base 2) fold change

I believe the most widely used method is to just set an adjusted P value and log (base 2) fold change cut-off, and to then 'throw' the resulting gene list into the GSEA without any ranking.

The lack of consensus on a proper filtering strategy may in part be due to the fact that a substantial proportion of researchers do not pay much attention to the results of GSEA. GSEA results would certainly never stand as the sole evidence in a clinical test, neither would they be sufficient evidence on which conclusions could be made in most reputable journals.

Kevin

ADD COMMENTlink modified 11 weeks ago • written 3.0 years ago by Kevin Blighe70k

what would be your answer if the question was about the GSEA program of Broad Institute?

ADD REPLYlink written 12 months ago by asalimih30

Rank by fold-change.

ADD REPLYlink written 12 months ago by Kevin Blighe70k

For others landing here, note also these excellent postings on using fGSEA:

ADD REPLYlink written 11 weeks ago by Kevin Blighe70k
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