Bioconductor does not provide Humane gene ST annotation "hugene10stv1cdf" to work with affylmGUI?!

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Prazeres da Costa Olivia ▴ 10

@prazeres-da-costa-olivia-3695

Last seen 10.3 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 • 1.4k views

ADD COMMENT • link updated 15.3 years ago by Marc Carlson ★ 7.2k • written 15.3 years ago by Prazeres da Costa Olivia ▴ 10

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Marc Carlson ★ 7.2k

@marc-carlson-2264

Last seen 8.4 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 • link 15.3 years ago Marc Carlson ★ 7.2k

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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 • link 15.3 years ago Peder Worning ▴ 100

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