[BioC] mirna102Xgaincdf package

[Marc Carlson]

Hi Xiaobin,

It sounds like you need a cdf package that is presently not supported
yet (I will look into this).  But in the meantime you should be able to
easily generate one if you look at the vignette found in of the
makecdfenv package.  You can see it in the documentation here:

http://www.bioconductor.org/help/bioc-views/release/bioc/html/makecdfenv.html


  Marc



On 01/28/2011 02:37 PM, Hooiveld, Guido wrote:
> Hi Xiaobin,
> Please keep this conversation on the list.
> No, the files you can download from Affymetrix are not an R-package; your really need a CDF environment for use in R. Ideally, the BioC core team will provide the R-version of this file, but for now I would suggest you specifically set the CDF environment as described here:
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/32287
> Thus, pointing R into the data dir, and then:
> affy.data <- ReadAffy(cdfname="mirna10")
> Be sure, however, to have these package installed:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("mirna10cdf", "mirna10probe")
>
> HTH,
> Guido
>
> From: Xiaobin Yuan [mailto:xiaobin.yuan at louisville.edu]
> Sent: Friday, January 28, 2011 20:56
> To: Hooiveld, Guido
> Subject: RE: [BioC] mirna102Xgaincdf package
>
> Hi Guido,
>
> Thanks for you reply. I downloaded file from :
>  http://www.affymetrix.com/support/downloads/library_files/miRNA-1_0_2xgain.zip.
>
> Can this file be treated as a R package.  I ran the set up but was told that some files are missing. It looks that this file is designed for other software not for R.
>
> thanks
> Xiaobin
>
>
>
>   
>>>> "Hooiveld, Guido" <Guido.Hooiveld at wur.nl<mailto:Guido.Hooiveld at wur.nl>> 1/28/2011 1:59 PM >>>
>>>>         
> Hi Xiaobin,
> Please see this thread:
> http://article.gmane.org/gmane.science.biology.informatics.conductor/32287
> and all (4) posts/replies therein.
>
> HTH,
> Guido
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> email:      guido.hooiveld at wur.nl<mailto:guido.hooiveld at wur.nl>
> internet:   http://nutrigene.4t.com
> http://www.researcherid.com/rid/F-4912-2010
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Xiaobin Yuan
> Sent: Friday, January 28, 2011 18:11
> To: bioconductor at r-project.org
> Subject: [BioC] mirna102Xgaincdf package
>
> Hi all,
>
> I have problem with the miRNA microarray from Affymetrix.       I got
> the following error message:
>
>   
>> data<-ReadAffy()
>> data
>>     
> AffyBatch object
> size of arrays=230x230 features (11 kb)
> cdf=miRNA-1_0_2Xgain (??? affyids)
> number of samples=5
> Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain miRNA-1_0_2Xgain Library - package mirna102xgaincdf not installed Bioconductor - mirna102xgaincdf not available In addition: Warning message:
> missing cdf environment! in show(AffyBatch)
>
> I could not find a new package named "mirna102xgaincdf" from BioConductor.
>
> thanks
>
> Xiaobin Yuan
>
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>
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