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List:       bioconductor
Subject:    [BioC] Custom CDF Version 12 is released
From:       Manhong Dai <daimh () umich ! edu>
Date:       2009-07-30 18:38:24
Message-ID: 1248979105.31129.54.camel () centos ! mbni ! med ! umich ! edu
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Hi,


	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.  

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

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