MSstats (version 2.4.0)

modelBasedQCPlots: Visualization for model-based quality control in fitting model

Description

To check the assumption of model, modelBasedQCPlots takes the results after fitting models from function (groupComparison) as input and automatically generate two types of figures in pdf files as output : (1) normal quantile-quantile plot (specify "QQPlot" in option type) for checking normally distributed errors.; (2) residual plot (specify "ResidualPlot" in option type) for checking constant variance among different features.

Usage

modelBasedQCPlots(data,type,axis.size=10,point.size=3,text.size=7,width=10, height=10,featureName=TRUE,feature.QQPlot="all",which.Protein="all",address="")

Arguments

data

'ModelQC' in testing output from function groupComparison.

type

choice of visualization. "QQPlots" represents normal quantile-quantile plot for each protein after fitting models. "ResidualPlots" represents a plot of residuals versus fitted values for each protein in the dataset.

axis.size

size of axes labels, e.g. name of the comparisons and of targeted proteins in heatmap, and name of the comparisons in comparison plot. Default is 10.

point.size

size of points in the graph for residual plots. Default is 3.

text.size

size of labeling for feature names only in normal quantile-quantile plots separately for each feature. Default is 7.

featureName

for "ResidualPlot" only, TRUE show feature labeling and FALSE means no feature legend printing.

feature.QQPlot

"all"(Default) means that one normal quantile-quantile plot will be generated with across features of a protein. "byFeature" will generate normal quantile-quantile plots separately for each feature of a protein.

width

width of the saved file. Default is 10.

height

height of the saved file. Default is 10.

which.Protein

Protein list to draw plots. List can be names of Proteins or order numbers of Proteins from levels(data$PROTEIN). Default is "all", which generates all plots for each protein.

address

the name of folder that will store the results. Default folder is the current working directory. The other assigned folder has to be existed under the current working directory. If type="residualPlots" or "QQPlots", "ResidualPlots.pdf" or "QQPlots.plf" will be generated. The command address can help to specify where to store the file as well as how to modify the beginning of the file name. If address=FALSE, plot will be not saved as pdf file but showed in window.

Details

Results based on statistical models are accurate as long as the assumptions of the model are met. The model assumes that the measurement errors are normally distributed with mean 0 and constant variance. The assumption of a constant variance can be checked by examining the residuals from the model.

• QQPlots : a normal quantile-quantile plot for each protein is generated in order to check whether the errors are well approximated by a normal distribution. If points fall approximately along a straight line, then the assumption is appropriate for that protein. Only large deviations from the line are problematic.
• ResidualPlots : The plots of residuals against predicted(fitted) values. If it shows a random scatter, then the assumption is appropriate.

The input of this function is "ModelQC" in the testing results from function (groupComparison). The example result is testResultMultiComparisons.

References

Ching-Yun Chang, Paola Picotti, Ruth Huttenhain, Viola Heinzelmann-Schwarz, Marko Jovanovic, Ruedi Aebersold, Olga Vitek. "Protein significance analysis in selected reaction monitoring (SRM) measurements." Molecular & Cellular Proteomics, 11:M111.014662, 2012.

Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek. "Statistical protein quantification and significance analysis in label-free LC-M experiments with complex designs" BMC Bioinformatics, 13:S16, 2012.

Examples

## 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")

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

head(testResultMultiComparisons$ModelQC)

# normal quantile-quantile plots
modelBasedQCPlots(data=testResultMultiComparisons$ModelQC,type="QQPlots",address="")

# residual plots
modelBasedQCPlots(data=testResultMultiComparisons$ModelQC,type="ResidualPlots",address="")