Overview
Liver toxicity dataset contains the expression measure of 3116 genes and 10 clinical measurements for 64 subjects (rats) that were exposed to non-toxic, moderately toxic or severely toxic doses of acetaminophen in a controlled experiment. The data come from a liver toxicity study (Bushel et al., 2007) in which 64 male rats of the inbred strain Fisher 344 were exposed to non-toxic (50 or 150 mg/kg), moderately toxic (1500 mg/kg) or severely toxic (2000 mg/kg) doses of acetaminophen (paracetamol) in a controlled experiment. Necropsy were performed at 6, 18, 24 and 48 hours after exposure and the mRNA from the liver was extracted. Ten clinical chemistry measurements of variables containing markers for liver injury are available for each subject and the serum enzymes levels are measured numerically. The data were further normalized and preprocessed by Bushelet al. (2007).
Usage in mixOmics
The liver toxicity dataset is implemented in mixOmics via liver.toxicity, and contains the following:
gene: data frame with 64 rows and 3116 columns. The expression measure of 3116 genes for the 64 subjects (rats).clinic: data frame with 64 rows and 10 columns, containing 10 clinical variables for the same 64 subjects.treatment: data frame with 64 rows and 4 columns, containing information on the treatment of the 64 subjects, such as doses of acetaminophen and times of necropsy.
We analyze these two data sets (genes and clinical measurements) using sPLS with a regression mode, in an attempt to explain/predict the clinical variables with respect to the gene expressions: