BScore                  BScore normalization
DRQualControl           Computing the dynamic range
LiWongRank              Li Wong rank / invariant probeset normalization
MannWhitney             Perform a Mann-Whitney test
RNAither-package        Statistical analysis of high-throughput RNAi
                        screens
RankProduct             Perform a Rank Product test
SNRQualControl          Computing the SNR
Ttest                   Perform a Student's t-test
ZPRIMEQualControl       Computing the Z' factor
ZScore                  ZScore normalization
ZScorePerScreen         ZScore normalization per experiment
ZScorePlot              Plot normalized intensity values per well
ZScorePlotTwo           Plot signal intensities per well (II)
channelPlot             Plot signal channels against each other
closestToZero           Return the replicate value closest to zero
compareHits             Searching for common hits between different
                        scoring methods
compareReplicaPlates    Compare replica plates
compareReplicateSD      Plot the standard deviation of replicates
compareReplicateSDPerScreen
                        Plot the standard deviation of replicates for
                        each experiment
compareReplicates       Compare replicate values
controlDensity          Plotting the control density
controlDensityPerPlate
                        Plotting the control density per plate
controlDensityPerScreen
                        Plotting the control density per experiment
controlNorm             Normalization on controls
createSubset            Creating a subset of a dataset according to a
                        certain column value
dataset                 a typical example RNAi dataset
datasetDrosophila       Genome-wide RNAi screen of cell viability in
                        Drosophila Kc167 cells by Boutros et al.
discardLabtek           Remove a complete plate from the analysis
discardWells            Remove wells from the analysis
divNorm                 Mean, median, ... , normalization
divideChannels          Divide channel values
eraseDataSetColumn      Remove columns from dataset
findReplicates          Find all replicates of a certain siRNA/gene in
                        a dataset
furthestFromZero        Return the replicate value furthest from zero
generateDatasetFile     Generate Dataset File
generateRepMatNoFilter
                        Generate a matrix of replicates (II)
generateReplicateMat    Generate a matrix of replicates
gseaAnalysis            Perform a GSEA analysis of a list of genes
header                  a typical header of an example RNAi dataset
headerDrosophila        the header of the genome-wide RNAi screen of
                        cell viability in Drosophila Kc167 cells by
                        Boutros et al.
hitselectionPval        Selecting hits according to p-values
hitselectionZscore      Selecting hits according to ZScores
hitselectionZscorePval
                        Selecting hits according to ZScores and
                        p-values
incorporatepValVec      Incorporate a vector of p-values into a dataset
indexSubset             Saving the indexes of a subset in the main
                        dataset
joinDatasetFiles        Join dataset files
joinDatasets            Join datasets
lowessNorm              Lowess normalization
mainAnalysis            Wrapper function for full automated analysis
makeBoxplot4PlateType   Generate a boxplot of the data per plate
makeBoxplotControls     Generate a boxplot of the data vs. the controls
makeBoxplotControlsPerPlate
                        Generate a boxplot of the data vs. the controls
                        for each plate
makeBoxplotControlsPerScreen
                        Generate a boxplot of the data vs. the controls
                        for each experiment
makeBoxplotPerPlate     Generate a boxplot of the data per plate
makeBoxplotPerScreen    Generate a boxplot of the data per experiment
multTestAdjust          Adjust p-values for multiple testing
numCellQualControl      Quality control of the number of cells
orderGeneIDs            Order a dataset
pValVec1                A vector of p-values after a median
                        normalization and a t-test
pValVec2                A vector of p-values after a Mann-Whitney test
percCellQualControl     Quality control of the percentage of cells
plotBar                 Plot signal intensities per well
plotControlHisto        Plot a histogram of the data values and
                        controls
plotControlHistoPerplate
                        Plot a histogram of the data values and
                        controls per plate
plotControlHistoPerscreen
                        Plot a histogram of the data values and
                        controls per experiment
plotHisto               Plot a histogram of the data values
plotHistoPerplate       Plot a histogram of the data values per plate
plotHistoPerscreen      Plot a histogram of the data values per
                        experiment
plotQQ                  Make a QQ plot
plotQQperplate          Make a QQ plot per plate
plotQQperscreen         Make a QQ plot per experiment
quantileNormalization   Quantile normalization
replicatesCV            Compute the correlation of variation (CV)
replicatesSpearmancor   Compute the correlation coefficient betwenn
                        replicates or experiments
rms                     Compute the replicate root mean square
rnaither                Wrapper function for full automated analysis
saveDataset             Save the normalized dataset into a dataset text
                        file
saveOldIntensityColumns
                        Save old intensity value columns
savepValVec             Save p-values to file
scoredDataset1          A dataset containing an additional column
                        showing the p-values, after a median
                        normalization and a t-test
scoredDataset2          A dataset containing an additional column
                        showing the p-values after a Mann-Whitney test
spatialDistrib          Generate spatial plots of intensity values
spatialDistribHits      Plotting the spatial distribution of the hits
subtractBackground      Background substraction
sumChannels             Summarize channels
summarizeReps           Generate a new dataset with summarized
                        replicates
summarizeRepsNoFiltering
                        Generate a new dataset with summarized
                        replicates
trim                    Compute the replicate mean with trimmed values
varAdjust               Variance adjustment
vennDiag                Plotting a Venn Diagram to compare hits
volcanoPlot             Making a volcano plot
