[BioC] CDF for miRNA-1_0_2Xgain (was: miRNA Array from Affymetrix)

[Hooiveld, Guido]

Hi Claudia,

Aha, that explains it.
For your info; we performed the miRNA arrays more than a year ago before this new FlashTag HSR kit was available, so this is new to me. However, since I *assume* the arrays that are used for hybridizations are still the same (in other words the content should be identical), you could make use of the suggestion Alex made (i.e. specifying the CDF environment to be used as per the example below).

The BioC core team takes responsibility for providing the CDF environments for all Affymetrix catalog arrays. When asked, James MacDonald (copied in this mail) was so kind to make availble the miRNA-1_0 CDF @ BioC, so I expect he doesn't mind doing so as well for this _2xgain cdf file. :)
http://www.affymetrix.com/support/downloads/library_files/miRNA-1_0_2xgain.zip

Regards,
Guido


> -----Original Message-----
> From: Claudia Döring [mailto:C.Doering at em.uni-frankfurt.de] 
> Sent: Monday, December 06, 2010 16:57
> To: Hooiveld, Guido
> Subject: AW: [BioC] miRNA Array from Affymetrix
> 
> Hi Guido,
> 
> I think the problem is, that we use the FlashTag HSR Kit from 
> Genisphere. In the technical documentation from Affymetrix is 
> a different library file (miRNA-1_0_2Xgain (to be used with 
> FlashTag HSR)) recommended.
> So, I need a CDF-file of this library file.
> 
> Sincerely
> 
> Claudia
> 



> -----Original Message-----
> From: bioconductor-bounces at r-project.org 
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Alex 
> Gutteridge
> Sent: Monday, December 06, 2010 17:06
> To: bioconductor at r-project.org
> Subject: Re: [BioC] miRNA Array from Affymetrix
> 
> Just to add on what Guido wrote, I had the same problem with 
> some CEL files I recently came across and manually setting 
> the CDF to mirna10 seemed to work fine. I've not found any 
> issues with annotation, so I'm assuming that while kludgy this is OK:
> 
> 
>     data = ReadAffy(celfile.path="../data/miRNA_raw_data/") data 
> 
> AffyBatch object
> size of arrays=230x230 features (40 kb)
> cdf=miRNA-1_0_2Xgain (??? affyids)
> number of samples=78
> 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) 
> 
>     data = 
> 
> ReadAffy(celfile.path="../data/miRNA_raw_data/",cdfname="mirna10")
> 
>     data 
> 
> AffyBatch object
> size of arrays=230x230 features (40 kb)
> cdf=mirna10 (7815 affyids)
> number of samples=78
> number of genes=7815
> annotation=mirna10
> notes=
> 
> --
> Alex Gutteridge
> 
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