Question: GSEA preranked list, values with same rank?
1
gravatar for janders8
4.0 years ago by
janders820
janders820 wrote:

Hi! I have a preranked list of genes that I'd like to run through GSEA. These are genes that correlate with a specific antibody responses, and are results that I have received from our bioinformatician (Spearman correlations). My problem is that the actual correlation coefficients for the genes are almost all the exact same number (either positive or negative)! How can this be and how will this affect how GSEA ranks the genes? Thanks!

gsea • 4.3k views
ADD COMMENTlink modified 4.0 years ago by Ming Tang2.6k • written 4.0 years ago by janders820
1
gravatar for Jean-Karim Heriche
4.0 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche24k wrote:

GSEA deals with ties by ranking them randomly so this may be a problem if you have many ties. See this page on how to use GSEA with a preranked list. I would also be suspicious of all correlation values being the same because this indicates you don't discriminate very well and the ranking may not be robust.

ADD COMMENTlink written 4.0 years ago by Jean-Karim Heriche24k

Ok, that was my understanding, too -- thanks for the help!

ADD REPLYlink written 4.0 years ago by janders820
1
gravatar for Ming Tang
4.0 years ago by
Ming Tang2.6k
Houston/MD Anderson Cancer Center
Ming Tang2.6k wrote:

I wrote a small post on GSEA http://crazyhottommy.blogspot.com/2016/08/gene-set-enrichment-analysis-gsea.html

ADD COMMENTlink written 4.0 years ago by Ming Tang2.6k
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