[BioC] Small bug in function 'countskip.FASTA.entries' from package altcdfenvs

[Lingsheng Dong]

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 at altern.org
>To: "Norman Pavelka" <norman.pavelka at unimib.it>
>CC: "Lingsheng Dong" <dong_lsh at hotmail.com>, bioconductor at 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
>
>