![[R logo]](../../../doc/html/logo.jpg)
| arrowProgress | Progress bar with an arrow |
| average | Average signal channels of a microarray experiment |
| average,EexprSet-method | 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 |
| createNewDBTable | Class "Sample" |
| createNewDBTable,Sample-method | Class "Sample" |
| createNewDBTable,SignalChannel-method | Micro array signal channel description |
| 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 |
| drawBioControls | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| drawBioControls,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| drawHistogram | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| drawHistogram,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| drawMA | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| drawMA,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| drawMA,exprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| drawMAPlot | Draw a standard MA plot |
| drawPolyAControls | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| drawPolyAControls,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| drawVolcanoPlot | Draw a volcano plot |
| EexprSet | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| EexprSet-class | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| format.latex | Formats strings to be LaTeX compliant |
| getA | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| getA,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| getAnnotation | Annotate a gene |
| getArrays | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| getArrays,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| getContentMatrix | Class "Sample" |
| getContentMatrix,Sample-method | Class "Sample" |
| getContentMatrix,SignalChannel-method | Micro array signal channel description |
| getData | Class "Similarity" |
| getData,Similarity-method | Class "Similarity" |
| getDistances | Class "Similarity" |
| getDistances,Similarity-method | Class "Similarity" |
| getEDB | Retrieving expression values from a database. |
| getM | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| getM,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| 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 |
| getPK,Sample-method | Class "Sample" |
| getSamplesFromDB | Lists all or only specified samples from the database. |
| getSignalChannels | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| getSignalChannels,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| getWeights | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| getWeights,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| isDecimal | Is the number a cardinal or a decimal number? |
| Layout-class | Micro array grid and print tip layout description object |
| loadFromDB | Load a Object from the database |
| loadFromDB,EexprSet-method | Load a Object from the database |
| loadFromDB,Sample-method | Load a Object from the database |
| 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 |
| plot,Similarity-method | Class "Similarity" |
| plotSimilarity | Draw a plot for the Similarity-class |
| print,Similarity-method | Class "Similarity" |
| progress | Progress bar |
| publishToDB | Writing the expression values from normalized micro arrays into a database |
| publishToDB,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| 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" |
| show,SignalChannel-method | Micro array signal channel description |
| SignalChannel-class | Micro array signal channel description |
| Similarity-class | Class "Similarity" |
| sort,Similarity-method | Class "Similarity" |
| toEexprSet | Transfor objects to objects of the type EexprSet |
| toEexprSet,MAList-method | Transfor objects to objects of the type EexprSet |
| toEexprSet,RGList-method | Transfor objects to objects of the type EexprSet |
| toExprSet | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| toExprSet,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| writeFigure | Includes a figure in a LaTeX document |
| writeLatexTable | Writes a matrix or data frame in latex format to a file. |
| writeTable | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |
| writeTable,EexprSet-method | Class "EexprSet" an extended verision of the "exprSet" class from "Biobase" |