Airway: Airway smooth muscle cells

In AliciaNieto/fdaRNA: RNA-Seq and Microarray Preprocessing

Description

Read counts per gene for airway smooth muscle cell lines RNA-Seq experiment. The dataset contains four cell lines in two conditions: control and treatment with dexamethasone. It consists of 29391 RNA's that have more than one nonzero values. About half of the RNA's of the original data had two or more samples with a zero value and were discarded.

Usage

data("Airway")

Format

A data frame with 29391 observations on the following 8 variables.

SRR1039508

a numeric vector

SRR1039509

a numeric vector

SRR1039512

a numeric vector

SRR1039513

a numeric vector

SRR1039516

a numeric vector

SRR1039517

a numeric vector

SRR1039520

a numeric vector

SRR1039521

a numeric vector

Details

Variables:

Col. odd: SRR1039508, SRR1039512, SRR1039516 and SRR1039520. Untreated data: control group.

Col. even: SRR1039509, SRR1039513, SRR1039517, SRR1039521. Treated data.

Source

Bioconductor. Package 'airway'.

References

Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky- Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. ’RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.’ PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.

Nieto-Reyes A, Cabrera J. Statistical depth based normalization and outlier detection of gene expression data. Preprint.

Examples

outlier.detection(Airway, clases = 2, Cla = list(c(1,3,5,7),c(2, 4, 6 ,8)), MS = TRUE)

AliciaNieto/fdaRNA documentation built on May 29, 2020, 11:58 a.m.