Question: What is the best way to rank genes for GSEA?
0
gravatar for Gabriel
4 weeks ago by
Gabriel20
Gabriel20 wrote:

I am doing pathway and gene ontology analysis using Gene Set Enrichment Analysis(GSEA). For the tools, you need to provide a ranked gene list, however, various papers have provide different recommendations on how to do this.

Is there a current consensus on what is the ideal way to do this? I've been using Log2 Fold change, and I am unsure weather to use Fold Change, p-values instead. Or an other method?

One post: Problem with creating GSEA rank file recommended signed p-values, but I haven't found any literature reviews or clarification on the issue. clusterProfiler mentions fold change for ranked gene lists, so I am unsure if I would be getting "bad results" by using p-value sorting. And if the different packages are optimized for one or the other sorting.

According to Yu, author of cluster profiler:

geneList contains three features: numeric vector: fold change or other type of numerical variable named vector: every number has a name, the corresponding gene ID sorted vector: number should be sorted in decreasing order https://github.com/GuangchuangYu/DOSE/wiki/how-to-prepare-your-own-geneList

"other type of numerical variable" is unclear. Perhaps there are other, similar methods to GSEA who have a more concrete way of doing things?

EDIT: for clusterProfiler's function gseGO() I get different result when using Log2FoldChange versus FoldChange for ranking

rna-seq go gsea gene ranking • 166 views
ADD COMMENTlink modified 4 weeks ago by Pietro50 • written 4 weeks ago by Gabriel20
2
gravatar for Pietro
4 weeks ago by
Pietro50
Italy
Pietro50 wrote:

Hi Gabriel

For GSEA, some they do signed fold change * -log10pvalue, found it here: http://crazyhottommy.blogspot.com/2016/08/gene-set-enrichment-analysis-gsea.html

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Pietro50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1035 users visited in the last hour