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

[Kasper Daniel Hansen]

A custom CDF file might not use all the probes on the array - I have  
no idea if the ones offered by Bioconductor does it. In that case,  
the check (might) fail.

Kasper

On Apr 12, 2007, at 8:18 AM, Henrik Bengtsson wrote:

> One could back up this by a calculation based on the assumption that
> there are (typically?) equal number of rows as columns on Affy arrays.
>  Anyone know of a counter example?
>
> /Henrik
>
> On 4/12/07, Francesco Ferrari <ferrari.francesco at unimore.it> wrote:
>> I found an interesting "trick" adopted within the package mtachprobes
>> to solve this problem...
>> i.e. obtaining chip dimensions information from current versions of
>> CDF packages.
>>
>> Within the package "matchprobes" there's a function named
>> ".lgExtraParanoia"
>>
>> If you read this function code you can find the following lines:
>> #############
>> tab = table(mm1 - pm1)
>> sizex = as.numeric(names(tab))[max(tab) == tab]
>> pm2 = pt$y * sizex + pt$x + 1
>> #############
>>
>> "mm1" is a vector containing MM probes indexes (obtained from CDF  
>> package)
>> "pm1" is a vector containing PM probes indexes (obtained from CDF  
>> package)
>> Then chip dimension (i.e. "sizex") is obtained as the maximum  
>> difference between
>> MM and PM probes indexes. This is based on the assumption that PM and
>> MM probe are usually next to each other on the chip
>> at same x coordinate and at adjacent y coordinates.
>> The last line is equal to function "xy2i()" since "pt" is a  
>> data.frame
>> containing probe sequences information
>> and columns x and y (i.e. vectors "pt$x" and "pt$y") contain xy  
>> probes
>> coordinates
>>
>>
>>
>> However I agree with the fact that this could not be the final  
>> solution
>> and that having dim environment accessible within CDF packages is a
>> better solution.
>>
>> Best,
>> Francesco
>>
>>
>>
>>
>>
>>
>>> Date: Wed, 11 Apr 2007 16:53:55 -0400
>>> From: "James W. MacDonald" <jmacdon at med.umich.edu>
>>> Subject: Re: [Bioc-devel] RFC: xy2i and i2xy in *cdf packages
>>> To: Seth Falcon <sfalcon at fhcrc.org>
>>> Cc: bioc-devel at stat.math.ethz.ch
>>> Message-ID: <461D4AE3.2070501 at med.umich.edu>
>>> Content-Type: text/plain;  charset="utf-8";  format=flowed
>>>
>>> Seth Falcon wrote:
>>>> Wolfgang Huber <huber at ebi.ac.uk> writes:
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> Rather than make up these new dimension objects in the CDF  
>>>>> package,
>>>>> why not teach the affy:indices2xy function to reach into the
>>>>> appropriate CDF package and grab the *unexported*, existing i2xy
>>>>> function in order to do its thing, and the affy:xy2indices to  
>>>>> grab the
>>>>> *unexported* xy2i function? Seems like the least intrusive way  
>>>>> to do
>>>>> things, and more flexible.
>>>>
>>>>
>>>> I don't think we should change the visibility of the xy2i functions
>>>> without going through the deprecation cycle.
>>>>
>>>> But in general, I like your suggestion.  Teaching affy to grab the
>>>> appropriate function seems sensible.  Personally, I think it is  
>>>> fine
>>>> to have these functions exported.  You can still get the right one
>>>> when using affy::xy2indices.  Symbol masking is a fact of R.
>>>>
>>>> But having the dimensions accessible in the CDF package also makes
>>>> sense to me and is easy so I'm still in favor of adding  
>>>> hgu95av2dim.
>>>> And the xy2i and i2xy functions should use it...
>>>
>>> The functions in affy don't care what happens with xy2i and i2xy  
>>> since
>>> they don't use them (they get dimensions directly from the  
>>> AffyBatch).
>>> The only functions that care are those that don't have an  
>>> AffyBatch to
>>> query.
>>>
>>> So, unless there are any objections*, I will add the little dim  
>>> env to
>>> the cdf packages any any functions that need this info (and don't  
>>> have
>>> an AffyBatch to query) will have to learn to use it.
>>>
>>> *By objections, I mean 'This will completely break my code and  
>>> destroy
>>> my life'. The cdf packages are nearing the end of their shelf lives,
>>> soon to be replaced with SQLite packages, so arguments about  
>>> stylistic
>>> differences and 'How things should be done' are counterproductive,
>>> especially given how close we are to release. Also, remember that  
>>> xy2i
>>> and i2xy are only being _deprecated_. Anybody who uses these  
>>> functions
>>> has > 6 months from now to make changes.
>>>
>>> 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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