Bioconductor does not provide Humane gene ST annotation "hugene10stv1cdf" to work with affylmGUI?!
1
0
Entering edit mode
@prazeres-da-costa-olivia-3695
Last seen 9.6 years ago
Dear all, I would like to use the affylmGUI package to analyze some Affymetrix Human Gene ST arrays. But it seems that Bioconductor does not provide the annotation package hugene10stv1cdf yet - which is needed to work with the affylmGUI library. I get the following error message: Error in getCdfInfo(object): Could not obtain CDF environment, problems encountered: Specified environment does not contain GuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available. How can I proceed to work with the affylmGUI package? Is there a "hugene10stv1cdf" annotation package available, and where do I have to install it, so that I can work with the affylmGUI library? Thanks for any help! Olivia [[alternative HTML version deleted]]
Annotation cdf affylmGUI Annotation cdf affylmGUI • 1.2k views
ADD COMMENT
0
Entering edit mode
Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.6 years ago
United States
Hi Olivia, Have you tried using the makecdfenf package to just generate the cdf package from the affy source cdf file? http://www.bioconductor.org/packages/devel/bioc/html/makecdfenv.html And the Affy source files are here: http://www.affymetrix.com/support/technical/byproduct.affx?product =hugene-1_0-st-v1 Marc Prazeres da Costa Olivia wrote: > Dear all, > > I would like to use the affylmGUI package to analyze some Affymetrix Human Gene ST arrays. But it seems that Bioconductor does not provide the annotation package hugene10stv1cdf yet - which is needed to work with the affylmGUI library. > > I get the following error message: > > Error in getCdfInfo(object): > Could not obtain CDF environment, problems encountered: > Specified environment does not contain GuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available. > > How can I proceed to work with the affylmGUI package? Is there a "hugene10stv1cdf" annotation package available, and where do I have to install it, so that I can work with the affylmGUI library? > > Thanks for any help! > Olivia > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENT
0
Entering edit mode
Dear List, I am working on developing a R-based method to use the replicated spots to automatically mark outlier spots and evaluate the quality of each hybridization. I am working with Exiqon arrays where we have four replicates of each probe on the arrays and the method works fine. But I would very much like to try it on other platforms with a different number of replicates of each probe, hopefully also higher than four. Do any of you have access to such data or know where to get it. I have tried the Gene Expression Omnibus, but I wasn't able to find any data with replicated spots. I need raw data and would vey much like to have a look at the pictures as well to evaluate the quality of the hybridizations. These data would mean a lot for development of our method. Thanks Peder Best regards Exiqon A/S Peder Worning, Ph.D. Senior Scientist, Biomarker Discovery Telephone: +45 45650457 Telefax: +45 45661888 E-mail: pwo at exiqon.com Bygstubben 3 DK-2950 Vedbaek Denmark www.exiqon.com The information transmitted is intended only for the per...{{dropped:9}}
ADD REPLY

Login before adding your answer.

Traffic: 876 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6