[Bioc-devel] Deprecation of xy2i and i2xy

[James W. MacDonald]

Hi Henrik,

Henrik Bengtsson wrote:
> Hi,
> 
> thanks for this.
> 
> Just a thought, would it be much work to also add a "chipType" value
> to containing the name of the original chip type.  Right now it is not
> possible to identify the original chip type given the package (or
> "clean" CDF name) - the mapping is in one direction only.  Example:
> 
>> cleancdfname("Mapping250K_Nsp")
> 
> [1] "mapping250knspcdf"'
> 
>> chipType("mapping250knspcdf")
> 
> [1] "Mapping250K_Nsp"
> 
> which would be handy when for instance looking up additional external
> annotation data/files given the CDF package etc.

Theoretically, not difficult. The existing mapping is simple, but 
mapping back is more difficult (e.g., where do you put the underscore? 
What gets capitalized?, etc), so you would really need something like an 
environment to do the mapping, and just keep that up to date by hand.

So it wouldn't be that difficult. However, as I noted yesterday, these 
packages are on their last legs so I don't want to put any more work in 
than necessary.

In addition, the mapping from Affy name to cleancdfname is to make 
programmatic things easier. The reverse mapping would simply be there to 
help the end user figure out what chip they are using. Fortunately, one 
of the things the human brain excels at is pattern matching, so figuring 
out that hgu133plus2 == HG-U133 Plus_2 is easy for someone to do. And 
really, if the end user doesn't know what chip (s)he is using, I don't 
think there is anything we can do to rectify that situation ;-D


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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