two.ways.stepback: Fitting a linear model by backward-stepwise regression

In mjnueda/maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

Description

two.ways.stepback fits a linear regression model applying backward-stepwise strategy.

Usage

two.ways.stepback(y = y, d = d, alfa = 0.05, family = gaussian(), epsilon=0.00001)

Arguments

y	dependent variable
d	data frame containing by columns the set of variables that could be in the selected model
alfa	significance level to decide if a variable stays or not in the model
family	the distribution function to be used in the glm model
epsilon	argument to pass to glm.control, convergence tolerance in the iterative process to estimate de glm model

Details

The strategy begins analysing a model with all the variables included in d. If all the variables are statistically significant (all the variables have a p-value less than alfa) this model will be the result. If not, the less statistically significant variable will be removed and the model is re-calculated. The process is repeated up to find a model with all the variables statistically significant (p-value < alpha). Each time that a variable is removed from the model, it is considered the possibility of one or more removed variables to come in again.

Value

two.ways.stepback returns an object of the class lm, where the model uses y as dependent variable and all the selected variables from d as independent variables.

The function summary are used to obtain a summary and analysis of variance table of the results. The generic accessor functions coefficients, effects, fitted.values and residuals extract various useful features of the value returned by lm.

Author(s)

Ana Conesa and Maria Jose Nueda, [e-mail]

References

Conesa, A., Nueda M.J., Alberto Ferrer, A., Talon, T. 2005. maSigPro: a Method to Identify Significant Differential Expression Profiles in Time-Course Microarray Experiments.

See Also

lm, step, stepfor, stepback, two.ways.stepfor

Examples

## create design matrix
Time <- rep(c(rep(c(1:3), each = 3)), 4)
Replicates <- rep(c(1:12), each = 3)
Control <- c(rep(1, 9), rep(0, 27))
Treat1 <- c(rep(0, 9), rep(1, 9), rep(0, 18))
Treat2 <- c(rep(0, 18), rep(1, 9), rep(0,9))
Treat3 <- c(rep(0, 27), rep(1, 9))
edesign <- cbind(Time, Replicates, Control, Treat1, Treat2, Treat3)
rownames(edesign) <- paste("Array", c(1:36), sep = "")
dise <- make.design.matrix(edesign)
dis <- as.data.frame(dise$dis)


## expression vector
y <- c(0.082, 0.021, 0.010, 0.113, 0.013, 0.077, 0.068, 0.042, -0.056, -0.232, -0.014, -0.040,
-0.055, 0.150, -0.027, 0.064, -0.108, -0.220, 0.275, -0.130, 0.130, 1.018, 1.005, 0.931,
 -1.009, -1.101, -1.014, -0.045, -0.110, -0.128, -0.643, -0.785, -1.077, -1.187, -1.249, -1.463)

s.fit <- two.ways.stepback(y = y, d = dis)
summary(s.fit)

mjnueda/maSigPro documentation built on Dec. 11, 2020, 12:21 a.m.