maDB-package | Package to store and retrieve microarray experiments into/from a database. |
arrowProgress | Progress bar with an arrow |
average | Average signal channels of a microarray experiment |
average-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 |
createFile | Create a file and all needed directories |
createJOINQuery | Create a SQL query that joins two or more tables |
createNewDBTable | Class "Sample" |
createNewDBTable-method | Class "Sample" |
createNewDBTable-method | Microarray 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 a list of all comparisons from the database |
dbGetExperimentInfo | List information about an experiment from the 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 |
doPlotSimilarity | Draw a plot for the Similarity-class |
drawHistogram | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
drawHistogram-method | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
drawMA | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
drawMA-method | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
drawMAPlot | Draw a standard MA plot |
drawVolcanoPlot | Draw a volcano plot |
format.latex | Formats strings |
getA | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getA-method | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getAnnotation | Annotate a gene |
getArrays | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getArrays-method | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getContentMatrix | Class "Sample" |
getContentMatrix-method | Class "Sample" |
getContentMatrix-method | Microarray signal channel description |
getData | Class "Similarity" |
getData-method | Class "Similarity" |
getDistances | Class "Similarity" |
getDistances-method | Class "Similarity" |
getEDB | Retrieving expression values from a database. |
getM | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getM-method | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getMDB | Retriev 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-method | Class "Sample" |
getSamplesFromDB | Lists all or only specified samples from the database. |
getSignalChannels | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getSignalChannels-method | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getWeights | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getWeights-method | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
isDecimal | Is the number a cardinal or a decimal number? |
Layout-class | Microarray grid and print tip layout description object |
loadFromDB | Load a dataset from the database |
loadFromDB-method | Load a dataset from the database |
loadFromDB-methods | Load a dataset from the database |
maDB | Package to store and retrieve microarray experiments into/from a database. |
MadbSet | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
MadbSet-class | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
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 |
newMadbSet | Create a new MadbSet object |
NormChips | example exprSet instance |
openMadbVignette | maDB vignette |
plotSimilarity | Draw a plot for the Similarity-class |
plotSimilarity-method | Draw a plot for the Similarity-class |
print-method | Class "Similarity" |
progress | Progress bar |
publishToDB | Writing the expression values from normalized micro arrays into a database |
publishToDB-method | Class "MadbSet" an extended version of the "ExpressionSet" 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 "Sample" |
Sample-class | Class "Sample" |
show-method | Microarray signal channel description |
SignalChannel-class | Microarray signal channel description |
Similarity-class | Class "Similarity" |
sort-method | Class "Similarity" |
writeFigure | Includes a figure in a LaTeX document |
writeLatexTable | Writes a matrix or data frame in latex format to a file. |
writeTable | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
writeTable-method | Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |