NanoStringGeoMxSet-class
                        Class to Contain NanoString Spatial Expression
                        Level Assays
aggregateCounts         Aggregate probe counts to target level for
                        feature data
checkQCFlags            Check QC Flags in the GeoMxSet and removes the
                        probe or sample from the object
checkQCFlags,NanoStringGeoMxSet-method
                        checkQCFlags
countsShiftedByOne      Accessor to check if "exprs" 'assDataElement'
                        was shifted by one
logtBase                Get take the log of a numeric vector
mixedModelDE            Run a mixed model on GeoMxSet
ngeoMean                Get the geometric mean of a vector
ngeoSD                  Get the geometric standard deviation of a
                        vector
normalize,NanoStringGeoMxSet-method
                        normalize
readDccFile             Read DCC File
readNanoStringGeoMxSet
                        Read 'NanoStringGeoMxSet'
readPKCFile             Read PKC File
setBackgroundQCFlags    Add background QC flags to NanoStringGeoMxSet
                        object protocol data
setBioProbeQCFlags      Add probe QC flags to NanoStringGeoMxSet object
                        feature data
setGeoMxQCFlags         Add GeoMx segment QC flags to
                        NanoStringGeoMxSet object protocol data
setQCFlags,NanoStringGeoMxSet-method
                        Add QC flags to feature and protocol data
                        simultaneously
setSegmentQCFlags       Add segment QC flags to protocol data
setSeqQCFlags           Add sequencing QC flags to NanoStringGeoMxSet
                        object protocol data
shiftCountsOne          Add one to all counts in an expression matrix
summarizeNegatives      Calculate negative probe summary stats
writeNanoStringGeoMxSet
                        write 'NanoStringGeoMxSet'
