Hi everybody,
I have a gene list (more than 6000 genes) and I would like to use GSEA, but it will only accept approximately 2990 genes? Does any one know how to fix it? Additionally, I would like compare my gene list with my own defined background, but I not sure how to do it in GSEA...
Thank you,
Best, Martin
1 answer
I have now downloaded the GSEA, but I have some problems in using my gene list. It is in text file. Can someone help me?
Best, Martin
I have my gene list (only gene names) in a txt-file, but I read that I have to change the format to others. And I can't really figure out, how to do it. When using GSEA online, it was so easy
Hi Lluis,
According to GSEA (http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats) the gene lists should be created using gmx or gmt. My lists contain only gene names, hence I was not sure how to convert my gene lists into gmx or gmt.
My background list is from an array card, but is defined according to my criteria. thank you
I have some problems in using my gene list.
Hold on, let me get my crystal ball and find out more about those problems.
Log in to answer this question.
-
Differences between GSVA and GSEA?
written by DS •
-
How to perform GSEA-preranked analysis with gene list from Machine Learning?
written by CBS •
-
Proper way of comparing list of mutated genes
written by nhaus •
-
Count, LT, PH, PT Column in Functional Annotation Chart of DAVID
written by nhaus •
-
GSEA Pre-ranked for an Overlapped Gene Set
written by bioinformatics2020
-
Doing GSEA analysis on a set of genes
written by c_u
-
Benjamin Hochberg adjust P-values
written by lampardmartin3 •
-
Gene function KEGG and GSEA
written by loly.pearl86 •
-
GSEA background list
written by insertname •
-
GSEA Preranked analysis on RNA-SEQ
written by Ron
How were you using GSEA? Online? You can also download a standalone version, to which you can probably add your own gene lists as well.
I was using it online...