diff --git a/NAMESPACE b/NAMESPACE
index 45ef657..43220b8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,13 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
+export(Grp2Analysis)
 export(MQtoMSstatsFormat)
 export(SRMService)
 export(getIntensities)
 export(getRequiredColumns)
 export(piwotPiw)
 export(plotNicely)
+exportClasses(Grp2Analysis)
 exportClasses(SRMService)
 import(DBI)
 import(methods)
 import(parallel)
 import(quantable)
+import(reshape2)
diff --git a/R/Grp2Analysis.R b/R/Grp2Analysis.R
index c5e9623..b73954c 100644
--- a/R/Grp2Analysis.R
+++ b/R/Grp2Analysis.R
@@ -1,12 +1,10 @@
 annotationColumns <- c("Raw.file","Condition", "BioReplicate", "Run","IsotopeLabelType")
 proteinColumns <- c("ProteinName","TopProteinName","nrPeptides")
 
-#'
+#' Perform 2 group analysis with visualization
 #' @export Grp2Analysis
 #' @exportClass Grp2Analysis
 #'
-#' @examples
-#' Grp2Analysis()
 Grp2Analysis <- setRefClass("Grp2Analysis",
                             fields = list( proteinIntensity = "data.frame",
                                            annotation = "data.frame",
diff --git a/R/SRMService.R b/R/SRMService.R
index 6e29339..f4e5064 100644
--- a/R/SRMService.R
+++ b/R/SRMService.R
@@ -195,13 +195,19 @@ SRMService <- setRefClass("SRMService",
                               )
                               return(int_)
                             },
+                            stripLabel=function(int_,light=FALSE){
+                              label<-if(light){.self$lightLabel}else{.self$heavyLabel}
+                              rownames(int_) <- gsub(paste("_",label,"$",sep=""),"",rownames(int_))
+                              invisible(int_)
+                            }
+                            ,
                             getMatchingIntensities = function(){
                               "get matrix with intensities, where nr of NAs in row < maxNA"
                               intLight_ <- .self$getTransitionIntensities(light=TRUE)
                               intHeavy_ <- .self$getTransitionIntensities()
 
-                              rownames(intLight_) <- gsub("_light$","",rownames(intLight_))
-                              rownames(intHeavy_) <- gsub("_heavy$","",rownames(intHeavy_))
+                              intLight_ <- stripLabel(intLight_, light=TRUE)
+                              intHeavy_ <- stripLabel(intHeavy_)
 
                               idx <-intersect(rownames(intLight_),rownames(intHeavy_))
 
diff --git a/inst/samples/grp2analysisTest.R b/inst/samples/grp2analysisTest.R
index 37045a2..2ee898c 100644
--- a/inst/samples/grp2analysisTest.R
+++ b/inst/samples/grp2analysisTest.R
@@ -2,6 +2,7 @@ rm(list=ls())
 
 protein <- read.csv("d:/googledrive/DataAnalysis/p2084/215579/proteinGroups.txt",sep="\t",stringsAsFactors = F)
 
+colnames(protein)
 
 rawF <-gsub("Intensity\\.", "", grep("Intensity\\.",colnames(protein),value=T) )
 
@@ -13,24 +14,11 @@ annotation <-data.frame(Raw.file = rawF,
                         IsotopeLabelType = rep("L",length(condition)), stringsAsFactors = F)
 
 
+library(SRMService)
 
-source("R/Grp2Analysis.R")
-
-
-grp2 <- Grp2Analysis(annotation, "p2084BlaBla", maxNA=8  , nrPeptides=3)
-grp2$setHeatmap("red")
-
+grp2 <- Grp2Analysis(annotation, "p2084BlaBla", maxNA=8  , nrPeptides=2)
 grp2$setMQProteinGroups(protein)
 
-grp2$getDesignMatrix()
-
-
 library(dScipa)
-idx <-grep("SL9B2_MOUSE",rownames(grp2$proteinIntensity))
-grp2$proteinIntensity[idx,]
-res.eb <- grp2$getPValues()
-head(res.eb)
-grep("SL9B2_MOUSE",rownames(res.eb))
-
 rmarkdown::render("inst/reports/Grp2Analysis.Rmd",output_format = "pdf_document", output_file = "Grp2Analysis.pdf")
 
diff --git a/man/Grp2Analysis-class.Rd b/man/Grp2Analysis-class.Rd
new file mode 100644
index 0000000..bee0cca
--- /dev/null
+++ b/man/Grp2Analysis-class.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Grp2Analysis.R
+\docType{class}
+\name{Grp2Analysis-class}
+\alias{Grp2Analysis}
+\alias{Grp2Analysis-class}
+\title{Perform 2 group analysis with visualization}
+\description{
+Perform 2 group analysis with visualization
+}
+\section{Methods}{
+
+\describe{
+\item{\code{getConditionData(condition)}}{get intensities as matrix for single condition}
+
+\item{\code{getNrNAs()}}{return number of NAs per protein}
+
+\item{\code{setMQProteinGroups(MQProteinGroups)}}{set MQ protein groups table}
+
+\item{\code{setProteins(protein)}}{used to verify proteingroups structure and set members}
+}}
+
diff --git a/man/SRMService-class.Rd b/man/SRMService-class.Rd
index e86d358..6d63390 100644
--- a/man/SRMService-class.Rd
+++ b/man/SRMService-class.Rd
@@ -25,52 +25,56 @@ The function performs a SQL query on the SQLite
 
 \item{\code{getNrNAs(light = FALSE)}}{show nr of NA's for heavy (defalt) or light transitions}
 
-\item{\code{getTransitionIntensities(light = FALSE)}}{get matrix with intensities, where nr of NAs in row < maxNA}
+\item{\code{getTransitionIntensities(maxNA, light = FALSE)}}{get matrix with intensities, where nr of NAs in row < maxNA}
 
-\item{\code{plotCommonTransitions(light = FALSE)}}{Shows transitions which occure in heavy and light}
+\item{\code{maxNAHeavy(max)}}{set maximum of na's heavy row}
 
-\item{\code{plotQValues()}}{show q value distribution for peak groups}
+\item{\code{maxNALight(max)}}{set maximum of na's in light row}
 
-\item{\code{setMaxNAHeavy(max = 0)}}{set maximum of na's heavy row}
+\item{\code{plotCommonTransitions(light = FALSE)}}{Shows transitions which occure in heavy and light}
 
-\item{\code{setMaxNALight(max = 0)}}{set maximum of na's in light row}
+\item{\code{plotQValues()}}{show q value distribution for peak groups}
 }}
 \examples{
+
 library(SRMService)
 tmp <- "D:/googledrive/DataAnalysis/p1930"
 allData <- read.csv( file=file.path(tmp,"data/longFormat.txt"),row.names = 1)
+head(allData)
 data <-allData
 pool=2
 data <-allData[allData$pool==pool,]
 head(data)
-srms <- SRMService(data,qvalue=0.25)
-
+srms <- SRMService(data,qvalue=0.05)
+SRMService$methods()
+srms$maxNAHeavy()
+SRMService$fields()
+head(srms$piw)
 
 srms$plotQValues()
 srms$plotTransition()
 srms$plotTransition(light=TRUE)
+
 srms$getNrNAs()
 srms$getNrNAs(light=TRUE)
-srms$maxNAHeavy
-srms$maxNALight
-
-srms$setMaxNAHeavy(30)
-srms$setMaxNALight(40)
+srms$maxNAHeavy()
+srms$maxNALight()
+srms$maxNAHeavy(80)
+srms$maxNALight(80)
+srms$plotCommonTransitions()
+srms$plotCommonTransitions(light=TRUE)
+tmp <-srms$getLHLog2FoldChange(maxNA = 20)
+srms$maxNAFC()
+resH <- srms$plotCommonTransitions()
+dim(resH)
+resL <-srms$plotCommonTransitions(light=TRUE)
+dim(resL)
+resAll <- srms$getMatchingIntensities()
+dim(resAll$light)
 
-colnames(srms$piw)
-head(srms$piw)
 tmpH <- srms$getTransitionIntensities()
-dim(tmpH)
-stopifnot(max(apply(tmpH, 1, function(x){sum(is.na(x))}))<=30)
 tmpL <- srms$getTransitionIntensities(light=TRUE)
 dim(tmpL)
-stopifnot(max(apply(tmpL, 1, function(x){sum(is.na(x))}))<=40)
-x<-srms$getMatchingIntensities()
-rownames(x$light)[1:10]
-
-
-tmp<-srms$getLHLog2FoldChange()
-head(tmp)
 
 }