fluExample {qusage}R Documentation

Example gene expression set

Description

This is a matrix containing microarray gene expression values taken from a publicly available dataset (GEO ID: GSE30550; Huang Y et al. PLoS Genet 2011). This dataset contains samples from 17 patients who were exposed to Influenza and had blood drawn approximately every 8 hours for a week. Patients were classified as either symptomatic (sx) or asymptomatic (asx) based on the severity of their symptoms.

The portion of the dataset included here contains a total of 15 time points, including a pre-exposure point (time 0) and points approximately every 8 hours up to 108 hours. eset.full is arranged by donor, and the information for each sample is contained in a table, flu.meta. The metadata table contains 7 columns:

SampleID

The GEO sample IDs, matching the column names of eset.full

Subject

the subject ID

Hours

The hour-post-infection that the sample was collected (stored as a factor)

Hours.Numeric

Same as above, but stored as a numeric vector

Condition

The condition of the donor, either symptomatic (sx) or asymptomatic (asx)

Gender

The donor gender

Age

Age of the donor at recruitment

Usage

  eset.full
  flu.meta

Format

eset.full is a matrix of gene expression measurements, with rows of genes and columns representing samples. flu.meta is a data frame, with rows of samples and columns of metadata information.

Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30550

References

Huang Y et al. (PLoS Genet 2011)


[Package qusage version 2.16.1 Index]