R help - Jul 2011 - filterMicroRna function: Sample replicates in preprocessing Agilent miRNA dataset

Hi,
I have a question about filterMicroRna in AgiMicroRna package function for
filtering probes in Agilent microRNA dataset.
>ddPROC = filterMicroRna(ddNORM.micro, dd, control = TRUE, IsGeneDetected =
TRUE, wellaboveNEG = FALSE, limIsGeneDetected = 75, limNEG = 25, makePLOT =
TRUE, target.micro, verbose = TRUE)
If in a dataset there are two or more sample replicates and in the step of
filtering probes I want to exclude a probe only if gIsGeneDetected = 0 in all
two or three sample replicates.

I don't think by 'filterMicroRna' function provides any option for
this type of filtering.

Are there any suggestions ? 

Thanks
Vickie S
 		 	   		  
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On Jul 28, 2011, at 3:33 PM, Vickie S wrote:
>
> Hi,
> I have a question about filterMicroRna in AgiMicroRna package  
> function for filtering probes in Agilent microRNA dataset.
>
>> ddPROC = filterMicroRna(ddNORM.micro, dd, control = TRUE,  
>> IsGeneDetected = TRUE, wellaboveNEG = FALSE, limIsGeneDetected =  
>> 75, limNEG = 25, makePLOT = TRUE, target.micro, verbose = TRUE)
>
> If in a dataset there are two or more sample replicates and in the  
> step of filtering probes I want to exclude a probe only if  
> gIsGeneDetected = 0 in all two or three sample replicates.
>
> I don't think by 'filterMicroRna' function provides any option
for
> this type of filtering.
>
> Are there any suggestions ?
Are you sure these are not BioConductor questions? They have their own  
sandbox.

-- 

David Winsemius, MD
West Hartford, CT