Custom Cdf For Affymetrix Human Genome U219 Array Plate?

Question

[Anthony Liekens]

I can't seem to find custom CDF files for Affymetrix' Human Genome U219 array plates. Can anyone point me in a direction?

Answer 1

[Houkto]

Hi there,

I usually get my own Custom CDF from Brain array website http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp I would suggest you give this Evolving Gene/Transcript Definitions Significantly Alter the Interpretation of GeneChip Data. Nucleic Acid Research 33 (20), e175. journal a good read as its explains why you need to use a custom cdf for affymetrix and their criteria used in generating. Someone might suggest that the journal published in 2005 however they have a website that release new versions of their custom cdf and you can see what's has been improved in each release, so it's on going research. When you decide you want to go with their custom files, you must choose what is your analysis will be based on e.g MIRBASEF, ENST (Transcripts) or REFSEQ (Refsequence) by going to this URl http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp and scroll down to their latest version (14.1), then you must specify which platform of R (statistic prog.) and which version of Bioconductor installed in it. R 2.13, BioC 2.8 <- this is the latest version of R and Bioconductor. once you click on the link of this version you will be directed on the species and chip type. In your case that will be Homo_sapiens and then HGU219. then you at the end of the line you will see different choices Custom CDF for R package column; underneath it: source column: for R that work under UNIX and R on Window platform. if you are running an analysis on R then you have to download C (Custom cdf file) and the P (probeset annotation) and then install them in R. if you are not running your analysis in R and you using a commercial software then you need to download the O (this will include the custom and annotation file for any other software that accept customatization like Partek.

I hope this will help you in your analysis. let me know how things will go