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?
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!
University of Washington/Fred Hutchinson Cancer Research Center
Seattle, WA USA