[Bioc-devel] affy's cleancdfname

[James W. MacDonald]

Seth Falcon wrote:
> On 26 Sep 2005, ririzarr at jhsph.edu wrote:
> 
> 
>>i believe that is what was intended. if the cdf name comes from an
>>enviromnent or an object in the workspace then it is assumed that
>>the correct name is given and it does not have to be inferred from
>>the information in the celfile.
>>
>>is someone having problems because of this?

Actually, there was a problem that someone came up with recently, and it 
is more of an inconsistency than anything else.

Say I don't have the wherewithal to create a cdf package, so I am just 
going to make the env and have it sitting in my .GlobalEnv.

hgfocuscdf <- make.cdf.env(dir()[11])
Reading CDF file.
Creating CDF environment
Wait for about 88 dots..................[snip]

Now I read in some HG-Focus celfiles.

 > dat <- read.affybatch(filenames=list.celfiles()[1:3])
Warning message:
Incompatible phenoData object. Created a new one.
   in: read.affybatch(filenames = list.celfiles()[1:3])

And I want to do something with the resulting AffyBatch.

 > dat
Error in library("hgfocuscdf", lib.loc = "C:/rw2020dev/library") :
         there is no package called 'hgfocuscdf'
AffyBatch object
size of arrays=448x448 features (4709 kb)
cdf=HG-Focus (??? affyids)
number of samples=3
Error in library("hgfocuscdf", lib.loc = "C:/rw2020dev/library") :
         there is no package called 'hgfocuscdf'
In addition: Warning message:
missing cdf environment ! in: show(list())

Since cdfFromEnvironment() is called without user intervention, there is 
no way for the end user to feed it the correct cdfname, and since it 
doesn't call cleancdfname(), it looks for 'HG-Focus', which doesn't 
follow the normal naming rules for a cdfenv. Therefore you either have 
to know a priori what getFromEnvironment() is going to look for, or you 
have to figure it out after the fact and rename your env.

Since none of the getFromXXX functions are actually called by the end 
user, I think they all have to use cleancdfname() to keep things 
consistent. This is the only way an end user has a fighting chance of 
getting the name of their env right.

There is another problem here that may be irrelevant given that Seth 
wants to deprecate reposTools. If I use remove.packages() to remove a 
BioC package (say, the hgfocuscdf package I removed for the above 
exercise), it doesn't remove anything from liblisting.Rda, so as far as 
reposTools is concerned, the package is still installed. getCdfInfo() 
went through all the getFromXXX functions and when it hit getFromBioC(), 
is.installed() said the package was installed, but since it isn't 
actually installed anymore it errored out.

Best,

Jim


-- 
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