Entry: EexprSet-class
Aliases: EexprSet-class drawBioControls,EexprSet-method drawBioControls drawHistogram,EexprSet-method drawHistogram drawMA,EexprSet-method drawMA drawMA,exprSet-method drawPolyAControls,EexprSet-method drawPolyAControls getArrays,EexprSet-method getArrays getA,EexprSet-method getA getM,EexprSet-method getM getSignalChannels,EexprSet-method getSignalChannels getWeights,EexprSet-method getWeights publishToDB,EexprSet-method toExprSet,EexprSet-method toExprSet writeTable,EexprSet-method writeTable EexprSet
Keywords: classes
Description: Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
URL: ../../../library/maDB/html/EexprSet-class.html

Entry: Layout-class
Aliases: Layout-class
Keywords: classes
Description: Micro array grid and print tip layout description object
URL: ../../../library/maDB/html/Layout-class.html

Entry: MAtoG
Aliases: MAtoG
Keywords: data
Description: Calculate the green intensity values from the M and A values given.
URL: ../../../library/maDB/html/MAtoG.html

Entry: MAtoR
Aliases: MAtoR
Keywords: data
Description: Calculate the red intensity values from the M and A values given.
URL: ../../../library/maDB/html/MAtoR.html

Entry: Sample-class
Aliases: Sample-class createNewDBTable,Sample-method getContentMatrix,Sample-method createNewDBTable getContentMatrix getPK,Sample-method
Keywords: classes
Description: Class "Sample"
URL: ../../../library/maDB/html/Sample-class.html

Entry: SignalChannel-class
Aliases: SignalChannel-class createNewDBTable,SignalChannel-method getContentMatrix,SignalChannel-method show,SignalChannel-method
Keywords: classes
Description: Micro array signal channel description
URL: ../../../library/maDB/html/SignalChannel-class.html

Entry: Similarity-class
Aliases: Similarity-class getData,Similarity-method getData getDistances,Similarity-method getDistances plot,Similarity-method print,Similarity-method sort,Similarity-method
Keywords: classes
Description: Class "Similarity"
URL: ../../../library/maDB/html/Similarity-class.html

Entry: arrowProgress
Aliases: arrowProgress
Keywords: data
Description: Progress bar with an arrow
URL: ../../../library/maDB/html/arrowProgress.html

Entry: average
Aliases: average,EexprSet-method average
Keywords: data
Description: Average signal channels of a microarray experiment
URL: ../../../library/maDB/html/average.html

Entry: calculateSimilarity
Aliases: calculateSimilarity
Keywords: data
Description: Calculate similarities (distances) between a vector and the rows (columns) of a matrix
URL: ../../../library/maDB/html/calculateSimilarity.html

Entry: checkForDifferentAnnotation
Aliases: checkForDifferentAnnotation
Keywords: data
Description: Detect gene annotation differences
URL: ../../../library/maDB/html/checkForAnnotation.html

Entry: createDirs
Aliases: createDirs
Keywords: data
Description: Create directories
URL: ../../../library/maDB/html/createDirs.html

Entry: createEexprSetFromLimma
Aliases: createEexprSetFromLimma
Keywords: data
Description: Changing a RGList or MAList into a object of the type EexprSet
URL: ../../../library/maDB/html/createEexprSetFromLimma.html

Entry: createFile
Aliases: createFile
Keywords: data
Description: Create a file and all needed directories
URL: ../../../library/maDB/html/createFile.html

Entry: createJOINQuery
Aliases: createJOINQuery
Keywords: data
Description: Create a SQL query that joins two or more tables
URL: ../../../library/maDB/html/createJOINQuery.html

Entry: createSampleFromTable
Aliases: createSampleFromTable
Keywords: data
Description: Create a new Sample object using data from a matrix
URL: ../../../library/maDB/html/createSampleFromTable.html

Entry: dbCalculateRegulations
Aliases: dbCalculateRegulations
Keywords: data
Description: Calculate regulation values from expression values in the database
URL: ../../../library/maDB/html/dbCalculateRegulations.html

Entry: dbGetComparisons
Aliases: dbGetComparisons
Keywords: data
Description: Get the information about the comparisons from the database
URL: ../../../library/maDB/html/dbGetComparisons.html

Entry: dbGetGeneRegulationRanking
Aliases: dbGetGeneRegulationRanking
Keywords: data
Description: Rank genes according to the number of comparisons they are regulated.
URL: ../../../library/maDB/html/dbGetGeneRegulationRanking.html

Entry: dbSearchSimilarPattern
Aliases: dbSearchSimilarPattern
Keywords: data
Description: Search for similar gene expression or regulation patterns in the database
URL: ../../../library/maDB/html/dbSearchSimilarPattern.html

Entry: deleteExperimentFromDB
Aliases: deleteExperimentFromDB
Keywords: data
Description: Deleting a experiment from a database.
URL: ../../../library/maDB/html/deleteExperimentFromDB.html

Entry: distance.euclidian
Aliases: distance.euclidian
Keywords: data
Description: Calculate vector similarity (distance) using euclidian distance metrics
URL: ../../../library/maDB/html/distance.euclidian.html

Entry: distance.pearson
Aliases: distance.pearson
Keywords: data
Description: Calculate vector similarity (distance) using pearsons correlation method
URL: ../../../library/maDB/html/distance.pearson.html

Entry: distance.pearson.uncentered
Aliases: distance.pearson.uncentered
Keywords: data
Description: Calculate vector similarity (distance) using (uncentered) pearsons correlation method
URL: ../../../library/maDB/html/distance.pearson.uncentered.html

Entry: distance.spearman
Aliases: distance.spearman
Keywords: data
Description: Calculate spearmans rank correlation between two vectors
URL: ../../../library/maDB/html/distance.spearman.html

Entry: drawMAPlot
Aliases: drawMAPlot
Keywords: data
Description: Draw a standard MA plot
URL: ../../../library/maDB/html/drawMAPlot.html

Entry: drawVolcanoPlot
Aliases: drawVolcanoPlot
Keywords: data
Description: Draw a volcano plot
URL: ../../../library/maDB/html/drawVolcanoPlot.html

Entry: format.latex
Aliases: format.latex
Keywords: data
Description: Formats strings to be LaTeX compliant
URL: ../../../library/maDB/html/format.latex.html

Entry: getAnnotation
Aliases: getAnnotation
Keywords: data
Description: Annotate a gene
URL: ../../../library/maDB/html/getAnnotation.html

Entry: dbGetAnnotation
Aliases: dbGetAnnotation
Keywords: data
Description: Annotate a list of IDs using the annotation table in the database.
URL: ../../../library/maDB/html/getDBAnnotation.html

Entry: getEDB
Aliases: getEDB
Keywords: data
Description: Retrieving expression values from a database.
URL: ../../../library/maDB/html/getExpValue.html

Entry: dbGetExperimentInfo
Aliases: dbGetExperimentInfo
Keywords: data
Description: List information about an experiment from a database.
URL: ../../../library/maDB/html/getExperimentDBInfo.html

Entry: getMDB
Aliases: getMDB
Keywords: data
Description: Retrieving regulation values from a database.
URL: ../../../library/maDB/html/getMDB.html

Entry: getPK
Aliases: getPK
Keywords: data
Description: Getting the primary key of the appropriate object from the database
URL: ../../../library/maDB/html/getPK.html

Entry: getPathFromFile
Aliases: getPathFromFile
Keywords: data
Description: Get the path to a file
URL: ../../../library/maDB/html/getPathFromFile.html

Entry: getSamplesFromDB
Aliases: getSamplesFromDB
Keywords: data
Description: Lists all or only specified samples from the database.
URL: ../../../library/maDB/html/getSamplesFromDB.html

Entry: isDecimal
Aliases: isDecimal
Keywords: data
Description: Is the number a cardinal or a decimal number?
URL: ../../../library/maDB/html/isDecimal.html

Entry: loadFromDB-methods
Aliases: loadFromDB-methods loadFromDB,EexprSet-method loadFromDB,Sample-method loadFromDB
Keywords: methods
Description: Load a Object from the database
URL: ../../../library/maDB/html/loadFromDB.html

Entry: multiapply
Aliases: multiapply
Keywords: data
Description: Apply a function to two arrays
URL: ../../../library/maDB/html/mapply.html

Entry: mean.center
Aliases: mean.center
Keywords: data
Description: Mean center a numerical vector
URL: ../../../library/maDB/html/mean.center.html

Entry: meanWithoutNA
Aliases: meanWithoutNA
Keywords: data
Description: Calculating the mean by excluding all NA and NULL values
URL: ../../../library/maDB/html/meanWithoutNA.html

Entry: medianWithoutNA
Aliases: medianWithoutNA
Keywords: data
Description: Calculating the median by excluding all NA and NULL values
URL: ../../../library/maDB/html/medianWithoutNA.html

Entry: multiGrep
Aliases: multiGrep
Keywords: data
Description: Perform a pattern search with a list of patterns
URL: ../../../library/maDB/html/multiGrep.html

Entry: myGrep
Aliases: myGrep
Keywords: data
Description: Perform a pattern search
URL: ../../../library/maDB/html/myGrep.html

Entry: plotSimilarity
Aliases: plotSimilarity
Keywords: data
Description: Draw a plot for the Similarity-class
URL: ../../../library/maDB/html/plotSimilarity.html

Entry: progress
Aliases: progress
Keywords: data
Description: Progress bar
URL: ../../../library/maDB/html/progress.html

Entry: publishToDB
Aliases: publishToDB
Keywords: data
Description: Writing the expression values from normalized micro arrays into a database
URL: ../../../library/maDB/html/publishToDB.html

Entry: replaceAll
Aliases: replaceAll
Keywords: data
Description: Replace all occurences of a specified character in a string by a new character
URL: ../../../library/maDB/html/replaceAll.html

Entry: replaces
Aliases: replaces
Keywords: data
Description: Replace all occurences of a specified character in a string by a new character
URL: ../../../library/maDB/html/replaces.html

Entry: NormChips
Aliases: NormChips
Keywords: data
Description: example exprSet instance
URL: ../../../library/maDB/html/smallALL.html

Entry: toEexprSet
Aliases: toEexprSet toEexprSet,RGList-method toEexprSet,MAList-method
Keywords: data
Description: Transfor objects to objects of the type EexprSet
URL: ../../../library/maDB/html/toEexprSet.html

Entry: dbUpdateAnnotation
Aliases: dbUpdateAnnotation
Keywords: data
Description: Create and update an annotation table in a PostgreSQL database.
URL: ../../../library/maDB/html/updateDBAnnotation.html

Entry: writeFigure
Aliases: writeFigure
Keywords: data
Description: Includes a figure in a LaTeX document
URL: ../../../library/maDB/html/writeFigure.html

Entry: writeLatexTable
Aliases: writeLatexTable
Keywords: data
Description: Writes a matrix or data frame in latex format to a file.
URL: ../../../library/maDB/html/writeLatexTable.html
