[BioC] Custom CDF Version 12 is released

[Groot, Philip de]

Hello all,

Again, I created full Bioconductor annotation libraries for a number of MBNI CustomCDF version 12 chips.
URL: http://nugo-r.bioinformatics.nl/NuGO_R.html

Entrezg (human, mouse, rat):
hgfocushsentrezg
hgu133a2hsentrezg
hgu133ahsentrezg
hgu133bhsentrezg
hgu133plus2hsentrezg
hgu95av2hsentrezg
hgu95bhsentrezg
hgu95chsentrezg
hgu95dhsentrezg
hgu95ehsentrezg
huex10stv2hsentrezg
hugene10stv1hsentrezg
mgu74av2mmentrezg
mgu74bv2mmentrezg
mgu74cv2mmentrezg
moe430ammentrezg
moe430bmmentrezg
moex10stv1mmentrezg
mogene10stv1mmentrezg
mouse4302mmentrezg
mouse430a2mmentrezg
nugohs1a520180hsentrezg
nugomm1a520177mmentrezg
rae230arnentrezg
rae230brnentrezg
raex10stv1rnentrezg
ragene10stv1rnentrezg
rat2302rnentrezg
rgu34arnentrezg
rgu34brnentrezg
rgu34crnentrezg
u133x3phsentrezg

TAIR (Arabidopsis):
ath1121501attairg
tilingatsnptilx520433attairg

If you need an annotation library that is lacking: just ask!

Regards,

Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl
Internet: http://www.nutrigenomicsconsortium.nl
             http://humannutrition.wur.nl
             https://madmax.bioinformatics.nl



-----Original Message-----
From: Manhong Dai [mailto:daimh at umich.edu]
Sent: Thu 30/07/2009 08:38 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Custom CDF Version 12 is released
 
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