BladderRepro: Dataset of Andersen et al (2004)

In NormqPCR: Functions for normalisation of RT-qPCR data

Description

This dataset was used in Andersen et al (2004) to demonstrate normalization of real-time quantitative RT-PCR data by geometric averaging of housekeeping genes.

Usage

data(BladderRepro)

Format

A qPCRBatch object which contains an expression matrix with the expression of 8 genes measured in 26 samples. The sample information is saved in the phenoData slot with variables

Sample.no.

sample number.

Grade

Grade of bladder cancer.

The following information on the measured genes is saved in the variables Symbol and Gene.name of the featureData slot.

CD14

CD14 antigen.

FCN1

Ficolin (collagen/fibrinogen domain containing) 1.

CCNG2

Cyclin G2.

NPAS2

Neuronal PAS domain protein 2.

UBC

Ubiquitin C.

CFL1

Cofilin 1 (non-muscle).

ACTB

Actin, beta.

GAPD

Glyceraldehyde-3-phosphate dehydrogenase.

For a detailed annotation see Table 1 and Supplementary table 1 in Anderson et al. (2004).

Details

This data set was used to check the reproducibility of the results obtained in Andersen et al (2004).

Source

The data set was obtained from http://www.mdl.dk/Publications_sup1.htm

References

Claus Lindbjerg Andersen, Jens Ledet Jensen and Torben Falck Orntoft (2004). Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets. CANCER RESEARCH 64, 5245-5250, August 1, 2004. http://cancerres.aacrjournals.org/cgi/content/full/64/15/5245

Examples

  data(BladderRepro)
  BladderRepro
  head(exprs(BladderRepro))
  pData(BladderRepro)
  fData(BladderRepro)

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