endotoxin {edge} | R Documentation

## Gene expression dataset from Calvano et al. (2005) Nature

### Description

The data provide gene expression measurements in an endotoxin study where four subjects were given endotoxin and four subjects were given a placebo. Blood samples were collected and leukocytes were isolated from the samples before infusion and at times 2, 4, 6, 9, 24 hours.

### Usage

    data(endotoxin)

### Format

- endoexpr: A 500 rows by 46 columns data frame containing expression values.

- class: A vector of length 46 containing information about which individuals were given endotoxin.

- ind: A vector of length 46 providing indexing measurements for each individual in the experiment.

- time: A vector of length 46 indicating time measurements.

### Value

endotoxin dataset

### Note

The data is a random subset of 500 genes from the full dataset. To download the full data set, go to http://genomine.org/edge/.

### 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

    library(splines)
    # import data
    data(endotoxin)
    ind <- endotoxin$ind
    class <- endotoxin$class
    time <- endotoxin$time
    endoexpr <- endotoxin$endoexpr
    cov <- data.frame(individual = ind, time = time, class = class)

    # formulate null and full models in experiement
    # note: interaction term is a way of taking into account group effects
    mNull <- ~ns(time, df=4, intercept = FALSE) + class
    mFull <- ~ns(time, df=4, intercept = FALSE) +
              ns(time, df=4, intercept = FALSE):class + class

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

    # 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)

[Package edge version 2.16.0 Index]