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
>
>
>
>
>
>
>
>
>
>
> This email message, including any attachments, is for the
...{{dropped}}
karsper is correct about oligo and makePlatformDesign. affy wont
handle
these data. with oligo you will be able to read in data and look at
probe level intensities. you can write your own scripts to analyze
this data. in a month or two we will add functionality to make calls
and do copy number analysis.
On Sep 9, 2005, at 12:28 AM, Kasper Daniel Hansen wrote:
> oligo
>>
>>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.
>>
>>
>>
>>
>>
If the 10K2_libraryfile.zip package contains the cdf file, i think
(but
i've never use it) that yhou can manage with the makecdfenv library.
try :
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("makecdfenv")
> library(makecdfenv)
> openVignette()
Please select (by number) a vignette
1: makecdfenv primer
2: affy primer
3: affy: Built-in Processing Methods
4: affy: Custom Processing Methods (HowTo)
5: affy: Automatic downloading of cdfenvs (HowTo):
6: affy: Import Methods (HowTo)
7: HOWTO access a repository
8: HOWTO set up a simple R repository
9: Biobase Primer
10: Howto Bioconductor
11: HowTo HowTo
12: eSet metadata structures
13: esApply Introduction
S?lection :
then choose 1 and have fun !
Julien
PS: if i said something wrong, please correct me!
