eset.full: Example gene expression set
In arcolombo/junk: qusage: Quantitative Set Analysis for Gene Expression

Description Usage Format Source References

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

1 2	eset.full flu.meta

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.

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

Huang Y et al. (PLoS Genet 2011)

arcolombo/junk documentation built on May 10, 2019, 12:49 p.m.