Bladder: Bladder dataset of Andersen et al (2004)

In jimrperkins/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(Bladder)

Format

A qPCRBatch object which contains an expression matrix with the expression of 14 genes measured in 28 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.

ATP5B

ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypetide.

HSPCB

Heat shock 90-kDa protein 1, beta.

S100A6

S100 calcium-binding protein A6 (calcylin).

FLOT2

Flotillin 2.

TEGT

Testis enhanced gene transcript (BAX inhibitor 1).

UBB

Ubiquitin B.

TPT1

Tumor protein, translationally controlled 1.

CFL1

Cofilin 1 (non-muscle).

ACTB

Actin, beta.

RPS13

Ribosomal protein S13.

RPS23

Ribosomal protein S23.

GAPD

Glyceraldehyde-3-phosphate dehydrogenase.

UBC

Ubiquitin C.

FLJ20030

Hypothetical protein FLJ20030.

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

Details

The genes included in this data set were selected by screening 99 bladder sample expression profiles.

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(Bladder)
  Bladder
  head(exprs(Bladder))
  pData(Bladder)
  fData(Bladder)

jimrperkins/NormqPCR documentation built on March 6, 2020, 1:06 a.m.