[BioC] Questions about gene identifiers and probesets regulation

[Chunyan Liu]

Dear all,

I'm doing gene expression comparisons between two groups of subjects
using affymetrix single-channel hgu133plus2 microarray chips and I have
two questions. 

1) Relationship among manufacturer ID, EntrezID, GenBank ID and gene
SYMBOL: Is there any one-to-one mapping?

I noticed that the hgu133plus2 environment gives annotations through
Entrez ID. Is this always the case? It seems to me that one EntrezID
corresponds to multiple manufacturer IDs (probe name), but is this the
case between manufacturer ID and GenBank ID? Is it true that one
EntrezID maps to one gene symbol? 

2) Probesets: Another question is after using limma, I get a list of
up- and down-regulated probeset when comparing two groups (1,000 up and
2,000 down regulated probesets). When I translate these into unique gene
symbols, I find 200 gene symbols that appear in both lists. Is this
plausible? Interpretable? 

Thank you very much for any input. 

Chunyan Liu
Cincinnati Children's Hospital