MiChip                  Introduction to the MiChip Package
boxplotData             Create Boxplot of data
boxplotDataNoFile       Create Boxplot of data
correctForFlags         Corrects for spots flagged as not present
myForgivingMedian       Produce Median from Probe Intensity values
naOmitMedian            Calculates the median of an array excluding NAs
normalizePerChipMedian
                        Normalize to median intensity
outputAnnotatedDataMatrix
                        Outputs a tab delimited file from an
                        ExpressionSet
panelCor                Add Pearson Correlation value to plots
parseRawData            Parse raw data files to create an ExpressionSet
plotIntensitiesScatter
                        Plot pairwise intensity scatter
removeUnwantedRows      Removes unwanted rows from data matrix
returnAnnotatedDataMatrix
                        returns and annotated data matrix from an
                        ExpressionSet
setIntensityCutoff      Sets a cutoff for the lowest intensity value
standardRemoveRows      Removes a standard list of features for MiChip
                        processing
summarizeIntensitiesAsMedian
                        Summarizes the probe intensity as median of
                        replicates spotted
workedExampleMedianNormalize
                        Worked Example of MiChip Processing
workedExampleNotNormalizedData
                        Worked Example of MiChip Processing
