Thanks for giving this clue, Lingsheng!
I was fearing something like that...

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 03:33, Lingsheng Dong wrote:

> Hi, Norman,
> I used 150 hours to match 29705 target sequences to HG-U95av2 probes 
> (640*640) on my PC with 500MHz processor. I think you will need two or 
> three more days to finish the matching.
> By the way, don't forget to save the matching result in a file as soon 
> as it is finished. I saved the object three times in case I lost it.
> Good luck.
>
> Lingsheng
>
> The fear of the LORD is the beginning of wisdom, and knowledge of the 
> Holy One is understanding.
> --Proverbs 10:10
>
>> From: Norman Pavelka <norman.pavelka@unimib.it>
>> To: lgautier@altern.org
>> 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 16:14:46 +0100
>>
>> 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
	[[alternative text/enriched version deleted]]

