Dear bioconductor mailing list, I need to compare several microarray platforms, for this I need consistent non-redundant annotation containing transcripts/genes. I began using the Brainarray CDFs which are available for a wide varity of platforms, icluding HG-U133A, HG-U133Plus2 and HG-U219 which I need. Now I know there are several other sources for custom CDFs. These include AffyProbeMiner ( http://gauss.dbb.georgetown.edu/liblab/affyprobeminer/links.html), AceView ( http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html) and Brainarray ( http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/gen omic_curated_CDF.asp). Also, there are *some publications* regarding the computation of new custom CDFs: A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences. BMC Genomics. 2007 Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays. BMC Bioinformatics. 2007 Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics, ( (2005) ) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res, ( (2005) ) Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics, ( (2004) ) Can someone please explain when it is best to use which one of the above? Or perhaps, when NOT to use one. Greetings, Andreas Heider [[alternative HTML version deleted]]