EexprSet-class          Class "EexprSet" an extended verision of the
                        "exprSet" class from "Biobase"
Layout-class            Micro array grid and print tip layout
                        description object
MAtoG                   Calculate the green intensity values from the M
                        and A values given.
MAtoR                   Calculate the red intensity values from the M
                        and A values given.
NormChips               example exprSet instance
Sample-class            Class "Sample"
SignalChannel-class     Micro array signal channel description
Similarity-class        Class "Similarity"
arrowProgress           Progress bar with an arrow
average                 Average signal channels of a microarray
                        experiment
calculateSimilarity     Calculate similarities (distances) between a
                        vector and the rows (columns) of a matrix
checkForDifferentAnnotation
                        Detect gene annotation differences
createDirs              Create directories
createEexprSetFromLimma
                        Changing a RGList or MAList into a object of
                        the type EexprSet
createFile              Create a file and all needed directories
createJOINQuery         Create a SQL query that joins two or more
                        tables
createSampleFromTable   Create a new Sample object using data from a
                        matrix
dbCalculateRegulations
                        Calculate regulation values from expression
                        values in the database
dbGetAnnotation         Annotate a list of IDs using the annotation
                        table in the database.
dbGetComparisons        Get the information about the comparisons from
                        the database
dbGetExperimentInfo     List information about an experiment from a
                        database.
dbGetGeneRegulationRanking
                        Rank genes according to the number of
                        comparisons they are regulated.
dbSearchSimilarPattern
                        Search for similar gene expression or
                        regulation patterns in the database
dbUpdateAnnotation      Create and update an annotation table in a
                        PostgreSQL database.
deleteExperimentFromDB
                        Deleting a experiment from a database.
distance.euclidian      Calculate vector similarity (distance) using
                        euclidian distance metrics
distance.pearson        Calculate vector similarity (distance) using
                        pearsons correlation method
distance.pearson.uncentered
                        Calculate vector similarity (distance) using
                        (uncentered) pearsons correlation method
distance.spearman       Calculate spearmans rank correlation between
                        two vectors
drawMAPlot              Draw a standard MA plot
drawVolcanoPlot         Draw a volcano plot
format.latex            Formats strings to be LaTeX compliant
getAnnotation           Annotate a gene
getEDB                  Retrieving expression values from a database.
getMDB                  Retrieving regulation values from a database.
getPK                   Getting the primary key of the appropriate
                        object from the database
getPathFromFile         Get the path to a file
getSamplesFromDB        Lists all or only specified samples from the
                        database.
isDecimal               Is the number a cardinal or a decimal number?
loadFromDB-methods      Load a Object from the database
mean.center             Mean center a numerical vector
meanWithoutNA           Calculating the mean by excluding all NA and
                        NULL values
medianWithoutNA         Calculating the median by excluding all NA and
                        NULL values
multiGrep               Perform a pattern search with a list of
                        patterns
multiapply              Apply a function to two arrays
myGrep                  Perform a pattern search
plotSimilarity          Draw a plot for the Similarity-class
progress                Progress bar
publishToDB             Writing the expression values from normalized
                        micro arrays into a database
replaceAll              Replace all occurences of a specified character
                        in a string by a new character
replaces                Replace all occurences of a specified character
                        in a string by a new character
toEexprSet              Transfor objects to objects of the type
                        EexprSet
writeFigure             Includes a figure in a LaTeX document
writeLatexTable         Writes a matrix or data frame in latex format
                        to a file.
