clippda (version 1.22.0)

sampleSize3DscatterPlots: A function for 3D display of sample size in a multi parameter space

Description

Displays the sample sizes computed using the clinically important parameters. This plot complements the contours plot.

Usage

sampleSize3DscatterPlots(Z,m,DIFF,VAR,beta,alpha,observedDIFF,observedVAR,observedSampleSize,Angle,Indicator)

Arguments

Z

the heterogeneity correction factor.

m

the number of replicates

DIFF

the clinically important difference.

VAR

the protein variance.

beta

the power to estimated the clinically important difference.

alpha

the significance level.

observedDIFF

the clinically important difference from your pilot data.

observedVAR

the clinically important variance from your pilot data.

observedSampleSize

the sample size estimated from your pilot data.

Angle

the angle for setting the orientation of the 3D-scatterplot.

Indicator

An indicator variable for controlling items to include in the plot. If it takes the value 1, then the parameters and sample size of previous proteomic profiling studies together with the results from your pilot study are plotted as points on the sample size calculation grid. If it is set to 0, then only the latter will be plotted.

Value

It returns a 3D plot of sample size against the variance versus differences.

References

1. Nyangoma SO, Ferreira JA, Collins SI, Altman DG, Johnson PJ, and Billingham LJ: Sample size calculations for planning clinical proteomic profiling studies using mass spectrometry. Bioinformatics, 2009, Submitted

2. Nyangoma SO, Collins SI, Douglas GW, Altman DG, Johnson PJ, and Billingham LJ: Issues in sample size calculations for designing cancer proteomic profiling studies. BMC Bioinformatics, 2009, Submitted

See Also

sampleSizeContourPlots

Examples

# the plot will be saved in your working directory

Z <- 2.460018

m <- 2

######

DIFF <- seq(0.1,0.50,0.01) 
VAR <- seq(0.2,4,0.1)
beta <- c(0.90,0.80,0.70)
alpha  <-  1 - c(0.001, 0.01,0.05)/2

####

observedDIFF  <-  0.4
observedVAR  <-  1.0
observedSampleSize  <-  80

#########
# indicator for including results of previous studies on the 3D plot.

Indicator  <-  1

# sets the orientation of the 3D plot.
 
Angle  <-  60    

sampleSize3DscatterPlots(Z,m,DIFF,VAR,beta,alpha,observedDIFF,observedVAR,observedSampleSize,Angle,Indicator)