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Published 20 hours ago • verified publisher icon sunduanchen

limma cameraPR

Open Able-Andy opened this issue 1 year ago • 2 comments

Hi guy, how to use CAMERA (function name: cameraPR) in the limma R package (v3.42.2) in the Pathway enrichment analysis?

Able-Andy avatar Mar 21 '23 12:03 Able-Andy

Hi

You can download the pathway gmt files from MSigDB and creat your own signature. Using the following code to run CAMERA.

hg_v6 <- readRDS(paste(rds_paths, gene_sets[i], sep = '/')) index <- ids2indices(hg_v6, DEG_result$Gene) camera <- cameraPR(signature, index)

Best, DS

On Tue, 21 Mar 2023 at 20:51, Able-Andy @.***> wrote:

Hi guy, how to use CAMERA54 (function name: cameraPR) in the limma R package (v3.42.2) in the Pathway enrichment analysis?

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sunduanchen avatar Mar 22 '23 02:03 sunduanchen

Could you please give me an example of the signature， index ，DEG_result$Gene？

Able-Andy avatar Mar 31 '23 03:03 Able-Andy