qPCRpros: Example processed qPCR data

Description Usage Format Examples

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

1

Format

The format is: Formal class 'qPCRset' [package ".GlobalEnv"] with 8 slots [email protected] 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\")" [email protected] assayData :<environment: 0x1180c9400> [email protected] phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. [email protected] varMetadata :'data.frame': 1 obs. of 1 variable: .. .. .. ..$ labelDescription: chr "Sample numbering" .. .. [email protected] data :'data.frame': 6 obs. of 1 variable: .. .. .. ..$ sample: int [1:6] 1 2 3 4 5 6 .. .. [email protected] dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. [email protected] .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. [email protected] .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 [email protected] featureData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. [email protected] varMetadata :'data.frame': 4 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:4] NA NA NA NA .. .. [email protected] 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 ... .. .. [email protected] dimLabels : chr [1:2] "featureNames" "featureColumns" .. .. [email protected] .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. [email protected] .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 [email protected] experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots .. .. [email protected] name : chr "" .. .. [email protected] lab : chr "" .. .. [email protected] contact : chr "" .. .. [email protected] title : chr "" .. .. [email protected] abstract : chr "" .. .. [email protected] url : chr "" .. .. [email protected] pubMedIds : chr "" .. .. [email protected] samples : list() .. .. [email protected] hybridizations : list() .. .. [email protected] normControls : list() .. .. [email protected] preprocessing : list() .. .. [email protected] other : list() .. .. [email protected] .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. [email protected] .Data:List of 2 .. .. .. .. .. ..$ : int [1:3] 1 0 0 .. .. .. .. .. ..$ : int [1:3] 1 1 0 [email protected] annotation : chr(0) [email protected] protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. [email protected] varMetadata :'data.frame': 0 obs. of 1 variable: .. .. .. ..$ labelDescription: chr(0) .. .. [email protected] data :'data.frame': 6 obs. of 0 variables .. .. [email protected] dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. [email protected] .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. [email protected] .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 [email protected] .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. [email protected] .Data:List of 3 .. .. .. ..$ : int [1:3] 2 14 0 .. .. .. ..$ : int [1:3] 2 14 0 .. .. .. ..$ : int [1:3] 1 3 0

Examples

1

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

HTqPCR documentation built on Nov. 1, 2018, 2:23 a.m.