[BioC] What to do with multiple probes?

[Vladimir Krasikov]

Sean Davis wrote:

>On 11/30/05 5:59 AM, "krasikov at science.uva.nl" <krasikov at science.uva.nl>
>wrote:
>
>  
>
>>Hi
>>Thanks Robert and Sean for your comments on my problem.
>>
>>
>>Robert Gentleman wrote:
>>    
>>
>>>Hi,
>>> Sean has already answered some of your questions, but I will provide a
>>>few of my thoughts on this.
>>>
>>> 1) there is little discussion because it is a reasonably difficult
>>>topic and there is not clear cut answers, besides "it depends" and it
>>>does depend on a lot of different things.
>>>
>>> For example, you might exclude the information on some probe sets if
>>>they are far from the poly-A tail and dT-priming was used, if random
>>>priming was used, then all should be equally good (but I am not aware of
>>>a comprehensive comparison).
>>>
>>> In some cases, depending on the data, processing etc, you can develp
>>>tools for comparing duplicate probe sets and combining the information
>>>to get better estimates for whether genes are expressed and at what
>>>levels (you could compare the probes and see if they are unique in the
>>>genome, for example). In these situations, using R is a good thing,
>>>since you can pretty much do any reasonable analysis, but you need to
>>>know some statistics and some programming to do it, and there is no
>>>clear recipe to follow.
>>>      
>>>
>>I have complete bacterial genome custom Agilent microarrays.
>>In my case custom means that we design all probes ourself (not Agilent),
>>with assigning quality-scores to the probes, and have tried to avoid
>>"poor" probes.
>>
>>The quality metrics for the probes should be equally good. It is random
>>priming experiment. This is an bacterial platform, so no tissue
>>specificity is possible, more over I may expect that there are not to
>>much biological variation between biological replicates.
>>
>>Taking into the account above  discussion about multiple probes, I guess
>>I can only make decisions individually gene-by-gene.
>>For that I can imagine the design in my point 2.
>>My question is: what kind of script should be to rearrange MAlist and
>>save it in text format?
>>    
>>
>
>Just to be clear--your multiple probes per gene are different and not
>identical for each gene?  If that is the case, then I think that you will
>need to write the script yourself, as I don't think one is available
>"off-the-shelf".  I would look at commands like "reshape", "split", and
>"aggregate" for good general purpose building blocks for jobs like this.
>
>Sean
>
>  
>
Yes my probes all unique - 1 to 3 per gene (8000 probes for 3000 genes).
I will try to do something,
unfortunately my programming and statistical background is rather low,
I afraid it would take from me to understand how to implement it in R 
too much time,
which I'm lacking now.
But I can do it in Excell (have some experience in visual basic).

Vladimir


-- 
Krasikov Vladimir
Universiteit van Amsterdam
Faculty of Science
IBED/AMB (Aquatische Microbiologie)
Nieuwe Achtergracht 127
NL-1018WS Amsterdam
the Netherlands

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