Question: Enrichment Score Calculation In Bioconductor
0
gravatar for Layla
6.9 years ago by
Layla50
Layla50 wrote:

Hi: I have a set of gene signatures obtained by SAM that contains data like this:

Gene ID     Score (sd)   
123456_at      45,5655
.......              ........

where Score is the t-statistics obtained.

The question that I have is based on that data, how I can obtain the enrichment score using bioconductor?

enrichment bioconductor • 4.4k views
ADD COMMENTlink modified 6.9 years ago by seidel6.8k • written 6.9 years ago by Layla50
2

Hi Marco Aurelio. Enrichment score of what? Do you mean GO term enrichment analysis? KEGG pathway enrichment analysis? Do you just want the p-value of your score? Try to be a bit more specific, and it will be easier to help you.

ADD REPLYlink modified 6.9 years ago • written 6.9 years ago by miquelduranfrigola760

I want to compare this list of genes with a data matrix that contains a set of probe sets ordered by their differential expression between healthy and disease samples.

ADD REPLYlink written 6.9 years ago by Layla50

If I have the set of up and down regulated genes as a signature from SAM, how can I compute an enrichment score for these genes, if I have only the t-statistics? thanks

ADD REPLYlink written 6.9 years ago by Layla50
4
gravatar for seidel
6.9 years ago by
seidel6.8k
United States
seidel6.8k wrote:

You could try the geneSetTest() function in the limma library (available at bioconductor). Given that you have gene signatures (i.e. a group of genes), and a healthy/disease data set, you can test your gene signature for significance in a data set as follows:

library(limma)
geneSetTest(gene_sig, dataset)

where gene_sig is a vector of indices representing the genes in your gene group that match genes in your data set, and dataset is your healthy/disease data ordered by some statistic (i.e. ratio or p-value).

ADD COMMENTlink written 6.9 years ago by seidel6.8k
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: 1155 users visited in the last hour