kidney: Gene expression dataset from Rodwell et al. (2004)

Description Usage Format Value Note References Examples

Description

Gene expression measurements from kidney samples were obtained from 72 human subjects ranging in age from 27 to 92 years. Only one array was obtained per individual, and the age and sex of each individual were recorded.

Usage

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Format

Value

kidney dataset

Note

These data are a random subset of 500 probe-sets from the total number of probe-sets in the original data set. To download the full data set, go to http://genomine.org/edge/. The age and sex are contained in kidcov data frame.

References

Storey JD, Xiao W, Leek JT, Tompkins RG, and Davis RW. (2005) Significance analysis of time course microarray experiments. PNAS, 102: 12837-12842.
http://www.pnas.org/content/100/16/9440.full

Examples

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# import data
data(kidney)
sex <- kidney$sex
age <- kidney$age
kidexpr <- kidney$kidexpr

# create model
de_obj <- build_study(data = kidexpr, adj.var = sex, tme = age,
sampling = "timecourse", basis.df = 4)

# use the ODP/lrt method to determine significant genes
de_odp <- odp(de_obj, bs.its=10)
de_lrt <- lrt(de_obj, nullDistn = "bootstrap", bs.its = 10)

# summarize significance results
summary(de_odp)

edge documentation built on Nov. 8, 2020, 6:48 p.m.