Lysis of M.tb Cells Example

DESCRIPTION:

This experiment was conducted to study the lysis of the bacteria M. tuberculosis in order the find a way to liberate more DNA. The experimental design was a mixed-level factorial with 4 experimental factors, namely, mf0412. One of the factors has 3 levels and the other three have two levels each. The design consists of 12 runs and is a 1/2 fraction of the full factorial. The response is the percent of DNA liberated compared to a gold standard.

ARGUMENTS:

temp
an experimental factor indicating the temperature of the reaction; namely, 25, 60 and 95 degrees C.
sonic
an experimental factor indicating the time of the reaction; namely, 0 minutes or 5 minutes.
edta
an experimental factor indicating the concentration of EDTA in the reaction buffer; namely, none or 1 mM.
bme
an experimental factor indicating the concentration of BME (beta-mercaptoethanol) in the reaction buffer; namely, none or 5 mM.
gpct
the response, percent hybridization of DNA compared to a "gold standard". Higher values are better.

SOURCE:

Experimental data provided by W. Keating of the Becton Dickinson Research Center, Research Triangle Park, NC. Used by permission of Becton Dickinson.

EXAMPLES:

# This design is already available in S-PLUS  
# under the name lysis.df. The following commands 
# were used to create the data frame: 
lysis.names<- list(temp=c(25,60,95),sonic=c(0,5), 
     edta=c(0,1),bme=c(0,5)) 
lysis.design <-design.digest('mf0412', lysis.names) 
lysis.gpct <- c(37.2,32.3,51.4,40.8,74.9,74.4,61.3, 
     86.3,87.4,100.2,139.3,153.2) 
lysis.df <- cbind(lysis.design,gpct=lysis.gpct) 
# sample analysis 
summary(lysis.df) 
lysis.fac <- fac.aov(lysis.df) 
summary(lysis.fac) 
pareto(lysis.fac) 
qqnorm(lysis.fac) 
tfiplot(lysis.fac,~temp:sonic) 
acplot(lysis.fac) 
acplot(lysis.fac,.4,5) 
ebplot(lysis.fac) 
lysis.rmod <- update(lysis.fac,. ~temp*sonic) 
pareto(lysis.rmod) 
plot(lysis.rmod)