designSampleSizePlots: Visualization for sample size calculation

In MeenaChoi/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Visualization for sample size calculation

Description

To illustrate the relationship of desired fold change and the calculated minimal number sample size which are (1) number of biological replicates per condition, (2) number of peptides per protein, (3) number of transitions per peptide, and (4) power. The input is the result from function (designSampleSize.

Usage

designSampleSizePlots(data, isPlotly = FALSE)

Arguments

data	output from function designSampleSize.
isPlotly	Parameter to use Plotly or ggplot2. If set to TRUE, MSstats will save Plotly plots as HTML files. If set to FALSE MSstats will save ggplot2 plots as PDF files

Details

Data in the example is based on the results of sample size calculation from function designSampleSize

Value

Plot for estimated sample size with assigned variable.

Author(s)

Meena Choi, Ching-Yun Chang, Olga Vitek.

Examples

# Based on the results of sample size calculation from function designSampleSize,
# we generate a series of sample size plots for number of biological replicates, or peptides, 
# or transitions or power plot.
QuantData<-dataProcess(SRMRawData)
head(QuantData$ProcessedData)
## based on multiple comparisons  (T1 vs T3; T1 vs T7; T1 vs T9)
comparison1<-matrix(c(-1,0,1,0,0,0,0,0,0,0),nrow=1)
comparison2<-matrix(c(-1,0,0,0,0,0,1,0,0,0),nrow=1)
comparison3<-matrix(c(-1,0,0,0,0,0,0,0,1,0),nrow=1)
comparison<-rbind(comparison1,comparison2, comparison3)
row.names(comparison)<-c("T3-T1","T7-T1","T9-T1")
colnames(comparison)<-unique(QuantData$ProteinLevelData$GROUP)

testResultMultiComparisons<-groupComparison(contrast.matrix=comparison, data=QuantData)

# plot the calculated sample sizes for future experiments:
# (1) Minimal number of biological replicates per condition
result.sample<-designSampleSize(data=testResultMultiComparisons$FittedModel, numSample=TRUE,
                                desiredFC=c(1.25,1.75), FDR=0.05, power=0.8)
designSampleSizePlots(data=result.sample)
# (2) Power
result.power<-designSampleSize(data=testResultMultiComparisons$FittedModel, numSample=2,
                               desiredFC=c(1.25,1.75), FDR=0.05, power=TRUE)
designSampleSizePlots(data=result.power)

MeenaChoi/MSstats documentation built on Nov. 30, 2024, 7:26 a.m.