how can I perform normalization and present/absent calls at the probe level of an Affymetrix experimental set?
I got data from an Affymetrix CGH chip (http://www.ebi.ac.uk/arrayexpress/arrays/A-AFFY-48). It was designed to test whole genome hybridization of several bacteria. It consists of 16 oligos for each predicted orf. Later on, expression experiments were performed with the same chip. Now I would like to know, if some of the probes are absent, i. e. in case of shorter transcripts.
With some Bioconductor packages, namely affy and makecdfenvs, I created a custom CDF package and was able to load the data. I could read the intensities of the probes of interest, but I'm not able to map them to the oligonucleotide sequences. I'm not sure, if the are in the same order as I expect it because IDs are only provided for the probe sets (or I could not find the probe IDs).
The question is now, how can I map the probe intensities to the oligo sequences (given with a probe set ID and X/Y coordinates i.e. Cbur00002_at:366:685). Okay, I got the answer myself. The MAGE-ML files are provided at EBI. I can use RMAGEML to import these files, at least theoretically. The RMAGEML seem to be outdated, at least the documentation.
Anyway, the normalization at the probe level and the mapping from RMAGEML/limma to the AffyBatch object is still unclear, as well as how to determine the presence/absence of parts of orfs.
Does anybody have some hints or a similar workflow?