In microarray analysis, we have the following problems, namely
1. Probes that do not have ENTREZ gene identifiers
2. Set of probes that map to the same ENTREZ gene id
3. Probes that are annotated as Affymetrix control probes, i.e. "AFFX-"
How should we deal with this probe? Is there a paper/book/software addressing this matter? Will the statistics and gene enrichment analysis be affected if you do not remove the above probes.