Function	Description
arrowProgress	Progress bar with an arrow
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
EexprSet-class	Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
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.
getPathFromFile	Get the path to a file
getPK	Getting the primary key of the appropriate object from the database
getSamplesFromDB	Lists all or only specified samples from the database.
isDecimal	Is the number a cardinal or a decimal number?
Layout-class	Micro array grid and print tip layout description object
loadFromDB-methods	Load a Object from the database
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.
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
multiapply	Apply a function to two arrays
multiGrep	Perform a pattern search with a list of patterns
myGrep	Perform a pattern search
NormChips	example exprSet instance
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
Sample-class	Class "Sample"
SignalChannel-class	Micro array signal channel description
Similarity-class	Class "Similarity"
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.