Question: GSEA - pathway analysis
0
gravatar for lampardmartin3
2.7 years ago by
lampardmartin30 wrote:

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

gene • 984 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by lampardmartin30
1

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.

ADD REPLYlink written 2.7 years ago by WouterDeCoster41k

I was using it online...

ADD REPLYlink written 2.7 years ago by lampardmartin30
0
gravatar for lampardmartin3
2.7 years ago by
lampardmartin30 wrote:

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

ADD COMMENTlink written 2.7 years ago by lampardmartin30
1

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

ADD REPLYlink written 2.7 years ago by Lluís R.860

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by lampardmartin30

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

ADD REPLYlink written 2.7 years ago by Lluís R.860

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

ADD REPLYlink written 2.7 years ago by lampardmartin30

I have some problems in using my gene list.

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

ADD REPLYlink written 2.7 years ago by WouterDeCoster41k
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: 2370 users visited in the last hour