[BioC] Custom CDF Version 12 is released

Manhong Dai daimh at umich.edu
Thu Jul 30 20:38:24 CEST 2009


	We just release Custom CDF Version 12 officially. 

	All files are available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp. All R packages are also in our own R repository. You should be able to use biocLite() to install them, just like other bioconductor packages.

	As a reminder, almost all Affymetrix chips are supported in Custom CDF. You can even use traditional method (ReadAffy and rma) to analyze latest gene chips, such as HuGene10stv1, HTHGU133PlusPM, etc.

	We also updated probeset web application that has all probe's genome location, user can input whatever probeset name to get sequence, chromosome and location. It is at http://arrayanalysis.mbni.med.umich.edu/probeset/.

	In addition, We released a R library 'CustomCDF' at http://arrayanalysis.mbni.med.umich.edu/MBNIUM.html#CustomCDF. The library has a few useful tools, such as retrieving probes that have a hit with snp, and removing them from cdf library on-the-fly, etc.

	By the way, our public WGAS is still using Custom CDF version 11, it should be updated in a few weeks.

	We want to thank Dr. De Bondt, An at Johnson & Johnson for finding a bug during preview.

Manhong Dai
The Molecular & Behavioral Neuroscience Institute (MBNI)
University of Michigan

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