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/genomic_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

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