Arguments for camera (gene set analysis)
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@clairenlevy-8745
Last seen 2.3 years ago
United States

Hi Bionconductors,

I've analyzed my microarray data for DE probes using limma and I'd like to use camera for gene set analysis, but I'm not quite sure I'm putting the right information in to the arguments. 

I am interested in whether genes in MSigDB Human C7 collection sets (downloaded from http://bioinf.wehi.edu.au/software/MSigDB/ ) are more DE compared to genes not in that set. Most of the DE probes that I found were in just one of the contrasts, so I'm just looking at that contrast.

With regard to the camera arguments, my questions are:

Is y supposed to be the exprs from the Eset that I used to do my DE analysis, i.e. the whole thing, NOT just exprs of the probes that were found to be DE in my contrast of interest?

For the index argument, if I am using ids2indices function, are the identifiers supposed to be the Entrez IDs of the probes that were DE in my contrast of interest?

Finally, in the result, does NGenes represent the number of genes from my input (index) that are also in that particular set?

Thanks in advance for your sage advice!

Claire Levy

University of Washington/Fred Hutchinson Cancer Research Center

Seattle, WA USA

 

camera GSEA • 2.4k views
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@gordon-smyth
Last seen 7 hours ago
WEHI, Melbourne, Australia

Any gene set testing analysis has to be done independently of the regular DE analysis. At no stage can you use information about which genes were individually DE, otherwise you will be double-dipping and the gene set p-values will be invalid.

'y' should be the same Eset that you passed to lmFit and eBayes for the regular DE analysis.

'index' simply identifies which genes are in each set. The 'identifers' are the gene IDs from 'y'.

'NGenes' is the number of genes in the set for which you have data, i.e., which correspond to a row of 'y'. It's the total size of the set.

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Great, thanks for the clarification and also for smoothing the way with the ids2indices function.

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@steve-lianoglou-2771
Last seen 21 hours ago
United States

Also, because we're talking about camera parameters here, I'll drop a link to this conversation about the inter.gene.cor parameter which was added somewhat recently:

C: Do the outputs of Limma's competitive gene set methods (camera, romer) require a

Which may be of use to the OP, but also to the next traveler who lands on this page by way of google.

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Thanks, I need to add that thread to my reading list!

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