[BioC] Importing CDF file for custom array using makecdfenv

[James W. MacDonald]

Jenny Drnevich wrote:
> Hi all,
> 
> Thanks Jim and Kasper for your responses. I'm still having trouble, and 
> I have a suggestion for changing the makecdfenv vignette...
> 
>>> I HOPE all the trouble I'm having below is related to this, and not 
>>> to me! Because the 'whatcdf' isn't working, I tried to get the cdf 
>>> name from an AffyBatch object:
>>>  > raw <- ReadAffy()
>>>  > raw at cdfName
>>> [1] "lund-zfa530237N"
>>
>>
>> Note here what the cdfname is. The affy package will look for this 
>> *exact* name when looking for the environment. Below, you call it 
>> something else:
>>
>> > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf")
>>
>> If you name it lund-zfa530237N, then everything should be copacetic.
> 
> 
> The reason I tried naming it "lundzfa530237ncdf" and then 
> "lundzfa530237n", not "lund-zfa530237N" is because the vignette, under 
> Section 4, Naming of CDF Packages and Environments, specifically says:
> 
> "The method getCdfInfo takes as an argument AffyBatch and returns the 
> appropriate environment. If x is an AffyBatch, this function will look 
> for an environment with name cleancdfname(x at cdfName)."
> 
> Perhaps this should be changed?  At any rate, I tried naming it 
> "lund-zfa530237N", but the "-" in the name is messing everything up:

Good point. The reason for the cleancdfname() function is to get rid of 
cruft like the "-" which will create the error you saw below. I will 
make some changes to the vignette that will hopefully make this clearer, 
and give a reasonable work around for situations like this.

Thanks for your input.

Best,

Jim



-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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