qPCRpros {HTqPCR}R Documentation

Example processed qPCR data

Description

Processed version of the raw data in qPCRraw, to be used as example data in the HTqPCR package. The data has been processed with setCategory to mark the feature categories, and with normalizeCtData using rank invariant normalisation.

Usage

data(qPCRpros)

Format

The format is: Formal class 'qPCRset' [package ".GlobalEnv"] with 8 slots ..@ CtHistory :'data.frame': 3 obs. of 1 variable: .. ..$ history: chr [1:3] "readCtData(files = exFiles$File, path = exPath)" "setCategory(q = qPCRraw, groups = exFiles$Treatment)" "normalizeCtData(q = qPCRpros, norm = \"norm.rankinvariant\")" ..@ assayData :<environment: 0x1180c9400> ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 1 obs. of 1 variable: .. .. .. ..$ labelDescription: chr "Sample numbering" .. .. ..@ data :'data.frame': 6 obs. of 1 variable: .. .. .. ..$ sample: int [1:6] 1 2 3 4 5 6 .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ featureData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 4 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:4] NA NA NA NA .. .. ..@ data :'data.frame': 384 obs. of 4 variables: .. .. .. ..$ featureNames: Factor w/ 191 levels "Gene1","Gene10",..: 1 104 115 126 137 148 159 170 181 2 ... .. .. .. ..$ featureType : Factor w/ 2 levels "Endogenous Control",..: 1 2 2 2 2 2 2 2 2 2 ... .. .. .. ..$ featurePos : Factor w/ 384 levels "A1","A10","A11",..: 1 12 18 19 20 21 22 23 24 2 ... .. .. .. ..$ featureClass: Factor w/ 3 levels "Kinase","Marker",..: 1 2 1 3 2 2 2 3 1 2 ... .. .. ..@ dimLabels : chr [1:2] "featureNames" "featureColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots .. .. ..@ name : chr "" .. .. ..@ lab : chr "" .. .. ..@ contact : chr "" .. .. ..@ title : chr "" .. .. ..@ abstract : chr "" .. .. ..@ url : chr "" .. .. ..@ pubMedIds : chr "" .. .. ..@ samples : list() .. .. ..@ hybridizations : list() .. .. ..@ normControls : list() .. .. ..@ preprocessing : list() .. .. ..@ other : list() .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 2 .. .. .. .. .. ..$ : int [1:3] 1 0 0 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ annotation : chr(0) ..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable: .. .. .. ..$ labelDescription: chr(0) .. .. ..@ data :'data.frame': 6 obs. of 0 variables .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. ..@ .Data:List of 3 .. .. .. ..$ : int [1:3] 2 14 0 .. .. .. ..$ : int [1:3] 2 14 0 .. .. .. ..$ : int [1:3] 1 3 0

Examples

data(qPCRpros)

[Package HTqPCR version 1.36.0 Index]