[BioC] What to do with multiple probes?

[Sean Davis]

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