[BioC] extracting one probe set

[Laurent Gautier]

James W. MacDonald wrote:
> Thomas Turner wrote:
> 
>> Dear all,
>>
>> I am trying to simply extract a table with the probe intensities for a 
>> probe set that I specify by name.  As described in 6.2 of the manual, 
>> I have been trying to use this command:
>>
>> ps <- probeset(affybatch, genenames = ("probe set name"))

This returns a 'list' of objects of class 'ProbeSet'.

To get the slot 'pm', there is no accessor function. One must use the 
'@' operator.


### R example
ps <- probeset(affybatch, genenames = ("probe set name"))
## return the 'pm' for the first probe set
ps[[1]]@pm
## return the 'pm' for all the probe sets
lapply(ps, function(x) x at pm)


> 
> Probably an easier method is to simply use the pm() and mm() accessor 
> functions.

...depends on what one wants to do...
...having things stored in a ProbeSet can let one use a couple of 
plotting methods, or 'express.summary.stat'...



L.



> pm(affybatch, genename)
> mm(affybatch, genename)
> 
> HTH,
> 
> 
> Jim
> 
>>
>> However, I am unable to make the following command work:
>> pm(ps[[1]])
>> If I ask R about my "ps", it gives me this:
>>
>> $"Ag.X.66.0 CDS s at"
>> ProbeSet object:
>>   id=Ag.X.66.0 CDS s at
>>   pm= 1 probes x  1  chips
>>
>> My affybatch includes four chips, which do not seem to be what this is 
>> telling me.  I am new to R, and any advice would be warmly received.
>>
>> Thank you,
>>
>> Tom Turner
>>
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> 
> 
>