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 1.42.0 Index]