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

[lgautier@altern.org]

> 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