[BioC] Please Help on how to install Mapping10K_XBa142 in R.

[Kasper Daniel Hansen]

Ok, you are using a 10k SNP chip.

What happens is that when you try to print (show) the data by typing
 > raw
the affy package expects to find what is called a cdf environment in  
order to do the printing. The SNP chips are a bit different from the  
standard gene expression chips, so metadata in the form of a cdf  
environment is not easily accessible from BioC (which is what it  
complains about, it discovers you have not installed a package  
containing environment and tries to do it for you.

If you need to work with SNP data I think you need the oligo package  
and the makePlatformDesign package. But that process is still a bit  
experimental, perhaps people with actual data analysis experience can  
chime in.

The affy library file contains a CDF _file_ which you need to read in  
using the makePlatformDesign package in order to create a relevant  
package.

Kasper



On Sep 8, 2005, at 3:19 PM, Zhang, Jacob ((Zhongfa)) wrote:

> Hi, everyone:
>
>
>
> I am just starting using Bioconductor Affy package. I have CEL file  
> and
> after read them, I got the error massage:
>
>
>
>
>> raw<-readaffy(),
>>
>
>
>> raw
>>
>
> Error in getCdfInfo(object) : Could not obtain CDF environment,  
> problems
> encountered:
>
> Specified environment specified did not contain Mapping10K_Xba142
>
> Library - package mapping10kxba142cdf not installed
>
> Data for package affy did not contain Mapping10K_Xba142
>
> Bioconductor - mapping10kxba142cdf not available
>
> AffyBatch object
>
> size of arrays=658x658 features (20301 kb)
>
> cdf=Mapping10K_Xba142 (??? affyids)
>
> number of samples=6
>
> Warning message:
>
> missing cdf environment ! in: show(list())
>
> Note: Using download type: Win32
>
> Error in getCdfInfo(object) : Could not obtain CDF environment,  
> problems
> encountered:
>
> Specified environment specified did not contain Mapping10K_Xba142
>
> Library - package mapping10kxba142cdf not installed
>
> Data for package affy did not contain Mapping10K_Xba142
>
> Bioconductor - mapping10kxba142cdf not available.
>
>
>
> As was pointed out, Bioconductor does not contain the mapping10KXBa  
> cdf
> file, my library does not contain the cdf file either.   I tried to
> install it by downloading the corresponding library from affy
> (10K2_libraryfile.zip,   but don't know how to install it in R.
>
>
>
>
>
> I know this may sound  routine for somebody, but it frustrated me a  
> lot,
> like....a blind person stumbling for a way out of darkness.....
>
>
>
> Thanks very much for your help. It means a lot of my time  being  
> saved.
>
>
>
> Jacob
>
>
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>
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> This email message, including any attachments, is for the ...{{dropped}}