create chip file
Biology Slideshow
Anthony Castanza
The CHIP file maps the gene identifiers used in your dataset to the gene identifiers used in your gene sets. If these identifiers match already you don’t need a chip file. If they don’t match, you’ll need to generate the mappings from a database that has them. This is typically some form of genomic resource for the organism of interest, for example Ensembl has data for Plasmodium here: https://protists.ensembl.org/Plasmodium_falciparum/Info/Index
You can probably retrieve gene mappings from their biomart for Plasmodium https://protists.ensembl.org/biomart/martview/0d26b5dbe676ef4b92067cefe44eebc3 but I don’t know what all data they have here.
The second column of a RNK file is the result from some sort of differential expression analysis, like Log2FC between two conditions. If you only have data from a single sample and not differential expression between two phenotypes, you might want to consider ssGSEA, an alternative form of GSEA offered through genepattern.org (https://gsea-msigdb.github.io/ssGSEA-gpmodule/v10/index.html)
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
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Anthony Castanza
Hello,
In the current version of GSEA, the parameter you’re looking for is “Collapse/Remap to gene symbols” and is under the first section “Required fields” as shown in the included screenshot:
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
From:
gsea...@googlegroups.com <gsea...@googlegroups.com> on behalf of Biology Slideshow <kazan.mo...@gmail.com>
Date: Saturday, March 20, 2021 at 12:39 PM
To: gsea...@googlegroups.com <gsea...@googlegroups.com>
Subject: Re: [gsea-help] create chip file
Actually I am using the latest version of GSEA app and my gene symbol are matching in geneset and dataset but i got error 1002
i could not find the parameter : "Collapse dataset to gene symbols parameter" to be set as false
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