I have groups of samples with copy-number variation (CNV) calls made based on microarray data. I am trying to determine if specific pathways are enriched with CNV for particular phenotypes. I've looked at How To Test Whether Copy Number Aberrations Are Enriched In A Gene List and other posts that describe pathway analysis from expression data. I currently have my data formatted for importing into PathVisio (tab-delimited file with genes as rows, columns are log transformed fold-change for each gene in each sample. If a gene was not overlapped by a CNV in a subject I assumed normal expression).
I have a few normal controls run with each batch, and each batch is a different phenotype. I'm trying to figure out the best way to determine if a pathway is enriched; should I compare pathway-X in sample1 to pathway-Y in sample1, should I compare pathway-X in phenotype1(all samples for a particular pathway averaged? summed?) to pathway-X in phenotype2, or should I do similar to the link above and generate random groups of genes of the same size as pathway-X and compare pathway-X in sample1 to randomly-generated-group-of-genes in sample1?
Statistics is not one of my strengths so any input is greatly appreciated.