[BioC] creating cdf environment Correction

[James W. MacDonald]

Carol Hannam wrote:
> OOPS - so sorry, but I made a mistake in copying the script of my previous
> email. Here is the correct version:
> 
> 
> Could someone please spot the error that I am making in creating a cdf
> environment?
> 
> 
>>library(affy)
>>library(makecdfenv)
>>pname<-cleancdfname(whatcdf("YY002001.cel"))
>>list(pname)
> 
> [[1]]
> [1] "xxxx007a46cdf"

There appears to be an oversight in the function getCdfInfo(). If you 
are using make.cdf.env(), you should name your env XXXX007a46 rather 
than using the cleancdfname. So basically change the line below to read

XXXX007a46 <- make.cdf.env("xxxx007a46.cdf")

and it should work for you.

NB: Note the error message below - although rather cryptic, it does 
state that it couldn't find the environment XXXX007a46, which was a 
subtle hint in the right direction.

Best,

Jim


> 
> 
>>xxxx007a46cdf<-make.cdf.env("xxxx007a46.cdf")
> 
> Reading CDF file.
> Creating CDF environment
> Wait for about 827 dots.......
> 
>>length(ls(xxxx007a46cdf))
> 
> [1] 82661
> 
>>eset<-justRMA()
> 
> Note: Using download type: Win32
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> encountered:
> Specified environment specified did not contain XXXX007a46
> Library - package xxxx007a46cdf not installed
> Data for package affy did not contain XXXX007a46
> Bioconductor - xxxx007a46cdf not available
> 
> Thanks for your help, again.
> C. Hannam
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623