gibson: Gene expression dataset from Idaghdour et al. (2008)

Description Usage Format Value Note References Examples

Description

The data provide gene expression measurements in peripheral blood leukocyte samples from three Moroccan groups leading distinct ways of life: desert nomadic (DESERT), mountain agrarian (VILLAGE), and coastal urban (AGADIR).

Usage

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Format

  • batch: Batches in experiment.

  • location: Environment/lifestyle of Moroccan Amazigh groups.

  • gender: Sex of individuals.

  • gibexpr: A 500 rows by 46 columns matrix of gene expression values.

Value

gibson dataset

Note

These data are a random subset of 500 genes from the total number of genes in the original data set. To download the full data set, go to http://genomine.org/de/.

References

Idaghdour Y, Storey JD, Jadallah S, and Gibson G. (2008) A genome-wide gene expression signature of lifestyle in peripheral blood of Moroccan Amazighs. PLoS Genetics, 4: e1000052.

Examples

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# import
data(gibson)
batch <- gibson$batch
gender <- gibson$gender
location <- gibson$location
gibexpr <- gibson$gibexpr
cov <- data.frame(Batch = batch, Gender = gender,
Location = location)

# create deSet for experiment- static experiment
mNull <- ~Gender + Batch
mFull <- ~Gender + Batch + Location

# create deSet object
de_obj <- build_models(gibexpr, cov = cov, full.model = mFull,
null.model = mNull)

# Perform ODP/lrt statistic to determine significant genes in study
de_odp <- odp(de_obj, bs.its = 10)
de_lrt <- lrt(de_obj, nullDistn = "bootstrap", bs.its = 10)

# summarize significance results
summary(de_odp)


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