Bladder: Bladder dataset of Andersen et al (2004)

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)

Arguments

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).

Source

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

Details

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

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

Run this code

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

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