Tuch: An example of real experiment.

In sSeq: Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

Description

A subset of the real experiment Tuch et al. It is used as an example for running some functions in this package.

Usage

data(Tuch)

Format

A data.frame containing 6 columns and 10453 rows.

Details

It compares the expression of genes in normal human tissues and in tissues with oral squamous cell carcinoma. The experiment had a paired design in that pairs of normal and tumor samples were obtained from three patient. The six libraries were sequenced using the SOLiD platform.

Source

The table of read counts was downloaded from GEO (accession GSE20116).

References

Tuch, B. et al. (2010). Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations. PloS One, 5, e9317.

Examples

data(Tuch);
head(countsTable);

Example output

Loading required package: caTools
Loading required package: RColorBrewer
             N8   N33   N51  T8  T33  T51
NM_000014  2242  2285 15121 261  597 1991
NM_144670 11731 13308  6944 912 3071 1160
NM_017436   162   111   751 296  362  182
NM_015665   199   215   512  81  344  342
NM_023928   470   573   690 710 1112  728
NM_024666   298   332   856 203  790  909

sSeq documentation built on Nov. 8, 2020, 5:52 p.m.