[Bioc-devel] RFC: xy2i and i2xy in *cdf packages

[Francesco Ferrari]

If xy2i() and i2xy() functions from CDF packages will be deprecated,
we could use the indices2xy() and xy2indices() functions from affy
package, but they require either "nr" parameter or an affybatch
object....

The "nr" parameter, i.e. the size of the chip, can't be obtained from
the other data conained in the CDF packages. Then, in order to use the
affy package functions we will have to load some CEL files into an
affybatch.

How can be addressed this issue?
Maybe an object containing these information (i.e. chip dimensions)
could be included into CDF packages.


Best regards,
Francesco


PS: I know that no package uses these functions, but we use them to
produce data for another package (work is still in progress). We could
use indices2xy() and xy2indices() functions from affy package, but the
value for "nr" parameter is required.








>
> Today's Topics:
>
>    1. Re: RFC: xy2i and i2xy in *cdf packages (James W. MacDonald)
>    2. Re: RFC: xy2i and i2xy in *cdf packages (Seth Falcon)
>
>
> Message: 1
> Date: Fri, 23 Mar 2007 09:22:56 -0400
> From: "James W. MacDonald" <jmacdon at med.umich.edu>
> Subject: Re: [Bioc-devel] RFC: xy2i and i2xy in *cdf packages
> To: lgautier at altern.org
> Cc: bioc-devel at stat.math.ethz.ch
> Message-ID: <4603D4B0.3030301 at med.umich.edu>
> Content-Type: text/plain;  charset="utf-8";  format=flowed
>
> Hi Laurent,
>
> lgautier at altern.org wrote:
> > Hi,
> >
> > Here is an RFC.
> >
> > Background:
> > The functions "xy2i" and "i2xy" are defined in each "cdf" annotation
> > package for Affymetrix arrays. The code for a particular package depends
> > on the
> > size of the corresponding array (e.g., for 133A2
> > xy2i = function(x,y) {y*732+x+1}
> > where 732 is the size of the array).
> >
> > Problem:
> > In the case one loads several such packages in the course of the same
> > session,
> > the function names are masking each others. This is a real danger as it
> > becomes too easy to call the "wrong" functions "xy2i" or "i2xy"
> > (both by functions that did not anticipate that several cdf packages could
> > be loaded in the same session, or by a user during an interactive
> > session).
>
> I know the affy package doesn't use these functions, and a quick grep of
> other packages that I thought might possibly use them came up empty as
> well. Do you know of any packages that use these functions?
>
> Given the fact that they do get masked on loading of other cdf packages,
> the apparent lack of use, and the existence of safer indices2xy() and
> xy2indices() functions, I would advocate deprecation/deletion rather
> than using a namespace.
>
> Best,
>
> Jim
>
>
> >
> > Proposed change:
> > - drop the functions "xy2i"/"i2xy" in the cdf packages and use of the
> > functions "indices2xy" or "xy2indices" in affy.
> >
> > *or*
> >
> > - hide "xy2i"/"i2xy" in the namespace of their respective packages,
> > enforcing an explicit function call (e.g., "hgu133a2cdf:::xy2i").
> >
> >
> > Regards,
> >
> >
> > Laurent
> >
> > _______________________________________________
> > Bioc-devel at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> --
> 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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>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 23 Mar 2007 07:01:37 -0700
> From: Seth Falcon <sfalcon at fhcrc.org>
> Subject: Re: [Bioc-devel] RFC: xy2i and i2xy in *cdf packages
> To: bioc-devel at stat.math.ethz.ch
> Message-ID: <m28xdo5a9q.fsf at ziti.fhcrc.org>
> Content-Type: text/plain; charset=us-ascii
>
> "James W. MacDonald" <jmacdon at med.umich.edu> writes:
> > I know the affy package doesn't use these functions, and a quick grep of
> > other packages that I thought might possibly use them came up empty as
> > well. Do you know of any packages that use these functions?
> >
> > Given the fact that they do get masked on loading of other cdf packages,
> > the apparent lack of use, and the existence of safer indices2xy() and
> > xy2indices() functions, I would advocate deprecation/deletion rather
> > than using a namespace.
>
> Laurent, thanks for bringing this up (I know it is something you
> mentioned in the past).  I like the idea of marking the functions in
> the cdfpackages using .Deprecated() for this release.  In the next
> cycle they can be .Defunct() and then gone.
>
> I realize it likely overkill, but sticking to the deprecation cycle is
> a good policy -- and if nobody is using them anyway, then the masking
> isn't going to bite anyone :-)
>
> Someone should send a note to the bioconducter list and announce that
> these functions will be deprecated in the upcoming release (and
> mention that there are alternatives in affy).
>
> Best,
>
> + seth
>
> --
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
> http://bioconductor.org
>
>
>
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> End of Bioc-devel Digest, Vol 36, Issue 19
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