Man pages for ArrayTools
geneChip Analysis Package

adjustmentAccess the multiple comparison adjustment method from the...
contrastMatrix-classClass to Contain the Contrast Matrix that Used for Linear...
createExpressionSetCreating an ExpressionSet
createGSEAFilesA Wrapper Function to create *.GCT and *.CLS for GSEA...
createIndexCreating an HTML index file
createIngenuityFileA Wrapper Function to Create Files for Ingenuity Analysis
designMatrix-classClass to Contain the Design Matrix that Used for Linear...
eSetExampleAn ExpressionSet example
exprsExamplea data.frame contains expression data
geneFilterfilter an ExpressionSet using different methods
getAdjPaccess the adjPVal slot from regressResult or...
getAnnotationaccess the annotation slot from the regressResult or...
getCompare1Access the Compare1 slot from the contrastMatrix
getCompare2Access the compare2 slot from the contrastMatrix class
getContrastAccess the contrast matrix from the contrastMatrix class
getCovariatesAccessing the covariates from the designMatrix class
getDesignAccess the design matrix from the designMatrix class
getFaccess the foldChange slot from regressionResult or...
getFCAccess the foldChange slot from the regressResult or...
getFCCutoffAccess the significantFCCutoff slot from the regressResult or...
getFilterMethodAccess the filterMethod slot from the regressResult or...
getIDaccess the ID slot from the regressResult or...
getIndexAccess the SignificantIndex slot from the regressResult or...
getInteractionAccess the interaction slot from the contrastMatrix class
getIntIndexAccess the IntIndex slot from the designMatrix class
getLengthCalculate the Length of interactionResult class
getLevelAccess the level slot from the contrastMatrix class
getNormalizationMethodAccess the significantIndex slot from the regressResult or...
getPAccess the pValue slot from regressResult or...
getPCutoffAccess the significantPvalueCutoff slot from regressResult or...
getTargetAccess the target slots from the designMatrix class
hugene10stCONTROLhugene10stCONTROL
interactionResult-classClass to Contain the Regression Result Based on An...
mogene10stCONTROLmogene10stCONTROL
Output2HTMLCreating HTML file for regressResult or interactionResult...
output.clsCreate *.CLS file for GSEA analysis
output.gctCreate an *.GCT file for GSEA analysis
output.ingCreate an Ingenuity File for Ingenuity Analysis
pDataExamplea phenoData example
postInteractionCreate an Object of InteractionResult Class for Testing...
preProcess3primeA wrapper function to normalize the the 3 prime array
preProcessGeneSTProprocess genechip ST array
qa3primeCreating Quality Assessment Report for 3 Prime Array
qaGeneSTCreating Quality Assessment Report for Gene ST Array
QCsample QC result from Affy Expression Console
regressRun regression to fit genewise linear model
regressionMethodAccess the regressionMethod slot from the regressResult or...
regressResult-classClass to Contain the Regression Result
selectSigGeneselect differentially expressed genes from the regressResult...
selectSigGeneIntselect differentially expressed genes from the...
SortSort a regressionResult or an interactionResult
ArrayTools documentation built on May 2, 2018, 3:04 a.m.