GSEA - pathway analysis

Question

[lampardmartin3]

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

[WouterDeCoster]

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.

[lampardmartin3]

I was using it online...

Answer 1

[lampardmartin3]

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

[Lluís R.]

Which problems do you have? Have you read the manual about the formats required to upload files (it can be a bit tricky)?

[lampardmartin3]

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

[Lluís R.]

Which errors do you get? To which format have you tried to convert it? What is you "own defined background" ?

[lampardmartin3]

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

[WouterDeCoster]

I have some problems in using my gene list.

Hold on, let me get my crystal ball and find out more about those problems.