Question: limma symbols2indices from gmt files versus rdata files
0
gravatar for biominer
3.9 years ago by
biominer10
European Union
biominer10 wrote:

Hello,

I'd like to do an enrichment using romer/roast/camera and my input are HGNC official human gene symbols.

For the symbols2indices() function I need a list of vectors for the reference gene sets, either from the rdata files provided by you or generated from the gmt-files from Broad institute.

As discussed previously in this post:

Romer and symbols2indices query

you had to curate the gene symbols in the gmt-files heavily to make them consistent, which is why you nicely provide these downloads. Does this all apply to the entrez-id gmts only or also to the gene-symbol gmts downloadable from Broad?

I wonder what is the better option, to use the gene symbol gmts or to map my ids to entrez first and use the rdata files. To my experience enrichments can be pretty vulnerable to how good the mappings work.

Do you have any experience with the gene-symbol version of the gmt-files? Or what would you recommend to do starting from HGNC-symbols (or ensembl gene ids)?

Best,

Maik

 

 

limma roast romer • 652 views
ADD COMMENTlink modified 3.8 years ago by Gordon Smyth39k • written 3.9 years ago by biominer10
Answer: limma symbols2indices from gmt files versus rdata files
2
gravatar for Gordon Smyth
3.8 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

Either way is fine.

Mapping official human symbols to Entrez Gene IDs is easy and pretty much one-to-one. That's what I would do.

Or working from the Broad Institute gene symbol gmts is also fine. It was different 6 years ago, but these days the symbol gmts from MSigDb contain official human symbols in a consistent format.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Gordon Smyth39k
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