Hi,

I'm new to R and BioC and I'm having a few issues.  I'm working with the AgiMicroRna package and so far I have normalised my data.  I haven't as yet filtered out the miRNAs that are not detected.  I have batch effects so I've used the ComBat script to correct the data - the result of which is that the data now consists of a single file containing just the probe names and a single value for each adjusted sample.  I want to filter out the non-detected miRNA as per the "filterMicroRna" function but this uses a bunch of parameters that I no longer have.  Can anyone suggest an alternative method that would produce the same effect?  Alternatively I can only think of making an individual file for each adjusted sample and manually adding back in the columns that I lost...I'm sure there must be an easier way.

Any input would be greatly appreciated,

Corrinne


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