Dear Bioconductor Community,
from a recent post in Bioconductor support forum (How to Find Common Dysregulated Genes in Two or More Sets of Microarray Data?) i found interesting also to try the GeneOverlap package, as i have aquired two DEG lists from different affymetrix microarray platforms from limma and treat, refering to the same comparison and disease(cancer colon samples vs control adjacent samples). But because im a beginner in R, i would like to ask two important questions:
Firstly, the function newGeneOverlap() requires anything else except the gene symbols from each list ?
Secondly, regarding the argument spec, which parameter should i use (("mm9.gene", "hg19.gene", "rn4.gene")) ??--
my two affymetrix platforms are hgu133a and hgu133plus2 .
Please excuse me for any naive questions