plotExp.cfa2way: Diagnostic plot of experimental replicates for two-way...

In CFAssay: Statistical analysis for the Colony Formation Assay

Description

This function plots the estimated means of a two-way ANOVA for each experiment in a series of plots. It is recommended to direct it in a pdf-file.

Usage

## S3 method for class 'cfa2way'
plotExp(x, labels=c(A="A",B="B"), ...)

Arguments

x	an R object of class cfa2way and resulting from function cfa2way.
labels	Labels for output description. These describe the meaning of A and of B.
...	further arguments to pass to generic function plotExp.

Author(s)

Herbert Braselmann

See Also

cfa2way

Examples

datatab<- read.table(system.file("doc", "exp2_2waycfa.txt", package="CFAssay"), header=TRUE, sep="\t")
names(datatab)  # has columns "x5fuCis" and "siRNA" 
fitcomp<- cfa2way(datatab, A="siRNA", B="x5fuCis", param="A/B")
print(fitcomp, labels=c(A="siRNA",B="x5fuCis"))
  pdf("TwoWay_experimental_plots.pdf")
    plotExp(fitcomp, labels=c(A="siRNA", B="x5fuCis"))
  dev.off()

Example output

[1] "Exp"       "x5fuCis"   "siRNA"     "ncells"    "ncolonies"
*** Two-way ANOVA for factors A and B with interaction *** 
A= siRNA , B= x5fuCis 
Test for interaction: F-test 
           F  Pr(>F)  
values 9.831 0.01202 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Use 'print' to see detailed results 

*** Logarithmic linear two-way ANOVA for factors A and B with interaction *** 
============================================================================= 
A= siRNA , B= x5fuCis 
Postscript digits for A or B: 0 inactive, 1 active 
surv_percent = exp(Estimate)*100 

Null hypothesis (Model 1): no interaction 
----------------------------------------- 
     Estimate Std. Error    t value     Pr(>|t|) surv_percent
A1 -0.4237844 0.06366051  -6.656944 5.660071e-05         65.5
B1 -1.1187559 0.07738539 -14.456939 4.980588e-08         32.7

Goodness-of-fit values 
	Residual Deviance: 77.99569 
	Total sum of squared weighted residuals ssqwresTot: 75.87275 
	Residual Degrees of Freedom: 10 
	Dispersion parameter: 7.587275 

Alternative hypothesis (Model 2): interaction 
--------------------------------------------- 
parametrization: A/B 
        Estimate Std. Error    t value     Pr(>|t|) surv_percent
A1    -0.3484218 0.05266374  -6.615972 9.746888e-05         70.6
A0:B1 -0.9757699 0.07170380 -13.608343 2.619891e-07         37.7
A1:B1 -1.3432352 0.09470322 -14.183627 1.832336e-07         26.1

Goodness-of-fit values 
	Residual Deviance: 37.15596 
	Total sum of squared weighted residuals ssqwresTot: 37.38767 
	Residual Degrees of Freedom: 9 
	Dispersion parameter: 4.154185 

Analysis of Variance Table and F-test
Model 2 versus Model 1
  Resid. Df Resid. Dev Df Deviance     F  Pr(>F)  
1        10     77.996                            
2         9     37.156  1    40.84 9.831 0.01202 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
png 
  2 

CFAssay documentation built on Nov. 8, 2020, 11:10 p.m.