[R] filterMicroRna function: Sample replicates in preprocessing Agilent miRNA dataset

[David Winsemius]

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