Hi Lingsheng,

Thanks for asking! But unfortunately I still didn't try to use those 
functions, because the 'matchprobes' routine finally gave its result 
only today! It took roughly 300 hours on my single-processor Mac G4 and 
150 hours on double-processor Linux machine, which sounds quite 
sensible.

I will start playing around with my brand new alternative CDF in the 
coming days and let you know... In the meantime, I suggest you to post 
a more specific question directly to the maintainer of the 'altcdfenvs' 
package, i.e. Laurent Gautier <lgautier@altern.org>. He's been always 
very kind in his replies...

Meanwhile, I have a new question for Laurent (or any other BioC 
contributor): "How can I make a CDF package from my brand new 
alternative CDF environment?"

I saw in the vignette of package 'makecdfenv' how to make a CDF 
environment or a CDF package starting from an Affy-provided CDF file, 
but not how to convert an already existing CDF environment into a CDF 
package... This would make it more easy for me to share it and also to 
track important information, such as package version, genome build, 
etc.

Does somebody have any idea that would be easy to implement with the 
existing packages? (For example, I hope I do not have to parse the 
content of my CDF environment into a Affy-like CDF file...)

Thanks in advance for any advice,
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 23 Nov 2005, at 17:59, Lingsheng Dong wrote:

> Hi, Morman,
> I still have difficulties to use the functions: "countduplicated", 
> "removeIndex" and "unique.CdfEnvAffy". The help files are not clear 
> either. Could you send me your script to call these functions?
> By the way, how are you doing with the "matchprobes" function ?
> Thanks.
>
> 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
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