Colon: Colon 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(Colon)

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).

Details

The genes included in this data set were selected by screening 161 colon 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(Colon)
  Colon
  head(exprs(Colon))
  pData(Colon)
  fData(Colon)

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