Colon: Colon 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(Colon)

Arguments

Format

A qPCRBatch object which contains an expression matrix with the expression of 13 genes measured in 40 samples. The sample information is saved in the phenoData slot with variables

Sample.no.: sample number.
Classification: Classification of colon cancer.

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

UBC: Ubiquitin C.
UBB: Ubiquitin B.
SUI1: Putative translation initiation factor.
NACA: Nascent-polypeptide-associated complex alpha polypeptide.
FLJ20030: Hypothetical protein FLJ20030.
CFL1: Cofilin 1 (non-muscle).
ACTB: Actin, beta.
CLTC: Clathrin, heavy polypeptide (Hc).
RPS13: Ribosomal protein S13.
RPS23: Ribosomal protein S23.
GAPD: Glyceraldehyde-3-phosphate dehydrogenase.
TPT1: Tumor protein, translationally controlled 1.
TUBA6: Tubulin alpha 6.

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 161 colon 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(Colon)
  Colon
  head(exprs(Colon))
  pData(Colon)
  fData(Colon)

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