based on some initial in vitro experiments, and a subsequent cancer microarray dataset analysis in R, i would like to perform some gene-set tests, for specific pathways and ontologies, regarding my phenotype of interest. Briefly, based on a two-group condition, we are mostly interested in identifying biological processes related to neutrophils, and subsequently more generally to inflammation. So the two major approaches under consideration:
A) Have identified through Gene Ontology Consortium, 7 GO-biological processes that are related to netrophils (http://amigo.geneontology.org/amigo/search/ontology?q=neutrophils)
B) The C7 immunologic signatures from WHEI (rdata files)
My major questions are:
1) In the context of microarrays, especially for the first part of the specific GOs: fry would be more appropriate, or mroast ? Alternatively,
would mroast be more suitable for the second part with the many immunologic gene sets ?
2) My second issue, is more specific with the microarray platform and annotation:
in detail, the microarray platform is the Agilent SurePrint G3 Human GE v2 8x60k Microarray (Array Design A-MEXP-2320),
for which as no R annotation package was available, i have downloaded the latest gene symbol annotation from https://earray.chem.agilent.com/earray/
Thus, as both of the above approaches need Entrez Gene ids, how could i proceed ? as my expression matrix, has unique gene symbols in the rows ? Below, is a small code chunk from the final limma part:
class(final) "EList" attr(,"package") "limma" dim(final$E) 23339 119 head(final$E) US84600244_253949426815_S01_GE1_107_Sep09_1_4 IRX1 4.979257 SAA1 7.548621 H19 13.150892 MBP 8.240486 SAA2 6.692976 CHGA 7.527782..... condition <- factor(final$targets$UBE2D3.group, levels = c("LOW.UBE2D3","HIGH.UBE2D3")) design <- model.matrix(~condition) fit <- lmFit(final,design)...
Thank you in advance,