geNorm: Data set of Vandesompele et al (2002)

In NormqPCR: Functions for normalisation of RT-qPCR data

Description

This data set was used in Vandesompele et al (2002) to demonstrate normalization of real-time quantitative RT-PCR data by geometric averaging of housekeeping genes.

Usage

data(geNorm)

Format

A qPCRBatch object which contains an expression matrix with 85 observations on the following 10 variables which stand for expression data of ten potential reference/housekeeping genes

ACTB

actin, beta

B2M

beta-2-microglobulin

GAPD

glyceraldehyde-3-phosphate dehydrogenase

HMBS

hydroxymethylbilane synthase

HPRT1

hypoxanthine phosphoribosyltransferase 1

RPL13A

ribosomal protein L13a

SDHA

succinate dehydrogenase complex subunit A

TBP

TATA box binding protein

UBC

ubiquitin C

YWHAZ

tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide

Details

The row names of this data set indicate the various human tissues which were investigated.

BM

9 normal bone-marrow samples

POOL

9 normal human tissues from pooled organs (heart, brain, fetal brain, lung, trachea, kidney, mammary gland, small intestine and uterus)

FIB

20 short-term cultured normal fibroblast samples from different individuals

LEU

13 normal leukocyte samples

NB

34 neuroblastoma cell lines (independently prepared in different labs from different patients)

Source

The data set was obtained from http://genomebiology.com/content/supplementary/gb-2002-3-7-research0034-s1.txt

References

Jo Vandesompele, Katleen De Preter, Filip Pattyn et al. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 2002. 3(7):research0034.1-0034.11. http://genomebiology.com/2002/3/7/research/0034/

Perkins, JR, Dawes, JM, McMahon, SB, Bennett, DL, Orengo, C, Kohl, M (2012). ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genomics, 13, 1:296.

Examples

  data(geNorm)
  str(exprs(geNorm.qPCRBatch))
  sampleNames(geNorm.qPCRBatch)

Example output

Loading required package: RColorBrewer
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: ReadqPCR
Loading required package: affy
Loading required package: qpcR
Loading required package: MASS
Loading required package: minpack.lm
Loading required package: rgl
Loading required package: robustbase

Attaching package: 'robustbase'

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

    rowMedians

Loading required package: Matrix
Warning messages:
1: In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
2: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
3: 'rgl_init' failed, running with rgl.useNULL = TRUE 
4: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
 num [1:10, 1:85] 0.0425 0.0576 0.1547 0.1096 0.118 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:10] "ACTB" "B2M" "GAPD" "HMBS" ...
  ..$ : chr [1:85] "BM1" "BM2" "BM3" "BM4" ...
 [1] "BM1"                "BM2"                "BM3"               
 [4] "BM4"                "BM5"                "BM6"               
 [7] "BM7"                "BM8"                "BM9"               
[10] "FIB1"               "FIB10"              "FIB11"             
[13] "FIB12"              "FIB13"              "FIB14"             
[16] "FIB15"              "FIB16"              "FIB17"             
[19] "FIB18"              "FIB19"              "FIB2"              
[22] "FIB20"              "FIB3"               "FIB4"              
[25] "FIB5"               "FIB6"               "FIB7"              
[28] "FIB8"               "FIB9"               "LEU1"              
[31] "LEU10"              "LEU11"              "LEU12"             
[34] "LEU13"              "LEU2"               "LEU3"              
[37] "LEU4"               "LEU5"               "LEU6"              
[40] "LEU7"               "LEU8"               "LEU9"              
[43] "NB1"                "NB10"               "NB11"              
[46] "NB12"               "NB13"               "NB14"              
[49] "NB15"               "NB16"               "NB17"              
[52] "NB18"               "NB19"               "NB2"               
[55] "NB20"               "NB21"               "NB22"              
[58] "NB23"               "NB24"               "NB25"              
[61] "NB26"               "NB27"               "NB28"              
[64] "NB29"               "NB3"                "NB30"              
[67] "NB31"               "NB32"               "NB33"              
[70] "NB34"               "NB4"                "NB5"               
[73] "NB6"                "NB7"                "NB8"               
[76] "NB9"                "POOL.brain"         "POOL.fetal.brain"  
[79] "POOL.heart"         "POOL.kidney"        "POOL.liver"        
[82] "POOL.lung"          "POOL.mammery.gland" "POOL.trachea"      
[85] "POOL.uterus"       

NormqPCR documentation built on Nov. 8, 2020, 6:37 p.m.