Grp2Analysis-class: Perform 2 group analysis with visualization
In protViz/SRMService: Report Quantitative Mass Spectrometry Data

Perform 2 group analysis with visualization

proteinIntensity: data.frame where colnames are Raw.File names, row.names are protein ID's and cells are protein abundances.
annotation_: annotations data.frame with columns such as Raw.File, Condition, Run etc.
proteinAnnotation: information about the proteins, nr of peptides etc.
nrPeptides: min number of peptides per protein
maxNA: maximum number of NA's
condition: summary of conditions
projectName: name of project
projectID: name of experiment
pvalue: pvalue threshold
qvalue: qvalue threshold
pfoldchange: foldchange threshold for p volcano plot
qfoldchange: foldchange threshold for q volcano plot
reference: document
removeDates: strip the date from file name.

getConditionData(condition): get intensities as matrix for single condition
getModPValuesCI(): get Pvalues and confidence intervals
getNormalized(): return normalized data
getNormalizedGrpAverages(): computes grp averages per protein
getNrNAs(): return number of NAs per protein
getResultTableWithPseudo(): add pseudo p-values and pseudo fold changes
getResultTableWithPseudoAndClustering(): calls getResultTableWithPseudo() and adds clusterID column
setMQProteinGroups(MQProteinGroups): set MQ protein groups table
setNormalizationMethod(normalizationMethod = "robustscale", housekeeper = ""): set the normalization parameters
setProteins(protein): used to verify proteingroups structure and set members