Gene Set Enrichment Analysis parameters
Hello,
As I mentioned in my previous question How to perform Gene Set Enrichment Analysis
I am trying to perform GSEA, I finally managed to build my data according to the structure of GSEA software from broadinstitute . Now I am trying to set the paramaters which I face a problem and I could not find a solution in the internet. The parameters are as follows:
Expression dataset
Gene sets database
Number of permutations
phenotype labels
collapse dataset to gene symbols
permutation tupe
chip platform
I don't know what to choose for the gene sets database. I selected one of those which appears by itself, but I get error. Anyone knows how to fix this ? or how to select the parameters?
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Mohammad, this is a follow up question which results from not following our advice from the previous question. If you had tried to come up with a suitable experimental question, some of these settings would be self explanatory. Unfortunately, you have denied to give us necessary information or have given misleading information about your experiment and its design. As I have previously suggested, it is possible that GSEA is not applicable in this case, but we cannot help you if you do not provide necessary information. Therefor I will close your question as not specific enough.
Hello Mohammad!
We believe that this post does not fit the main topic of this site.
See my comment above...
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!
Hello Michael,
Thanks for your time. I appreciate all the help I receive from this website. I think I was clear enough in my previous post (I have built the expression dataset gene and the phenotype ) of course the question was the up and down regulated of genes. The main reason I created this post because I could not find any information related how to select the parameters for GSEA software which I believe many people are using it in the field. However, if you think my question was not suitable enough, then I have nothing to say!
Once more thank you so much for your time and I am so happy to find this website because it helps me to learn so many things
Cheers
GSEA does not address the question of up and down regulated genes. Differential expression analysis (DE) does. GSEA is not hypothesis free, DE is (only hypotheses some genes are differentially expressed). Have a look at the documentation of the limma R-package to establish this.
No, unfortunately not.