As far as I can see, these three functions are all part of package 
'altcdfenvs'.
Thus, for a help on the functions, simply type:

library(altcdfenvs)
?countduplicated
?removeIndex
?unique.CdfEnvAffy

To see the source code, simply type the name of the function (without 
any brackets) and ENTER!

Good luck!
Norman

Norman Pavelka
Department of Biotechnology and Bioscience
University of Milano-Bicocca
Piazza della Scienza, 2
20126 Milan, Italy

Phone: +39 02 6448 3556
Fax: +39 02 6448 3552

On 17 Nov 2005, at 01:05, Lingsheng Dong wrote:

> Dr. Gautier,
> Please give some clue where we can find the description of these 
> functions or even the souce code.
> Thank a lot.
>
> Lingsheng
>
> The fear of the LORD is the beginning of wisdom, and knowledge of the 
> Holy One is understanding.
> --Proverbs 10:10
>
>> From: lgautier@altern.org
>> To: "Norman Pavelka" <norman.pavelka@unimib.it>
>> CC: "Lingsheng Dong" <dong_lsh@hotmail.com>, 
>> bioconductor@stat.math.ethz.ch
>> Subject: Re: [BioC] Small bug in function 'countskip.FASTA.entries' 
>> from      package altcdfenvs
>> Date: Wed, 16 Nov 2005 16:55:21 +0100 (CET)
>>
>> > Hi Lingsheng,
>> >
>> > On 15 Nov 2005, at 19:05, Lingsheng Dong wrote:
>>
>> <snip>
>>
>> >> Still another problem you may want consider:
>> >> The "matchprobes" function gives all possible matches. In my case, 
>> a
>> >> lot of probes match hundreds of target sequences. It means there 
>> will
>> >> be too many crossing hybredization probes if you put all probes
>> >> matching a target sequence into one probe set.
>> >> I couldn't find a ready to use funciton to solve this problem yet. 
>> I
>> >> am thinking to export the matching result into a database software 
>> and
>> >> manually delete crossing hybridezaiton probes.
>> >> Not sure if this a quick solution.
>> >> Hope you can give some suggetion.
>> >
>> > I also thought of that problem, but Laurent Gautier already gave 
>> some
>> > clues in his BMC Bioinformatics paper on how to handle this 
>> situation.
>> > Though I still didn't try, I guess that everything could be done 
>> very
>> > quickly inside R, without the need of exporting into an external
>> > database. If you like, I can share with you my experience, as soon 
>> as I
>> > have done some trials...
>>
>> The functions "countduplicated", "removeIndex", and 
>> "unique.CdfEnvAffy"
>> are your friends.
>>
>> Hoping this helps,
>>
>> Laurent
	[[alternative text/enriched version deleted]]

