Dear Laurent,

On 16 Nov 2005, at 16:55, lgautier@altern.org wrote:

>> 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
>

Thanks for pointing to these functions! I will give a trail as soon as 
the 'matchprobes' routine is over...

BTW, I launched the script 150 hours ago, but it's still not finished. 
How much computational time should I foresee to need on my standard Mac 
G4 machine (OS X Panther)? Here are some number to have an idea: I'm 
remapping the MOE430 v2.0 arrays (approximately 1 million probes) 
against roughly 38000 unique EnsEMBL transcripts...

Thank you in advance for your feed-back!

Best,
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
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