Problem:

I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the Flybase file required to do so (as described here) but I have noticed that most of the FBgn's have more than one associated Affy id.

My question is, how do I know which to assign to my data? From the list of affy-ids that I have, how do I label each one with the appropriate FBgn? I am using data from the Ayroles et al 2009 (DGRP) which has a column of AffyID which look similar to the ones in the Flybase file but shorter (1638273_at). Perhaps I don't grasp why there would be more than one.

Some have one affy id which is repeated across 15 columns in the file, whereas some seem to have several affy id's associated with them.

Required:

Question 1: Why does a singular FBgn identifier have more than one associated affy identifier?

Question 2: Why do some datasets, such as the dataset I have, have shorter versions of the affy identifier?

Question 3: Where can I find an up to date and appropriate list matching these Affy id's the FBgn identifiers correctly?