@@ -257,7 +257,6 @@ getData <- function(input) {

       } else {

         label = "LF"

       }

-      print(label)

       mydata = MaxQtoMSstatsPTMFormat(evidence=mydata,

                                       annotation=annotation,

                                       input$fasta$datapath,

@@ -365,13 +364,13 @@ getData <- function(input) {

                                          use_unmod_peptides=use_unmod_peptides)

     }else {

-      data = read.csv(input$msstatsptmdata$datapath, header = TRUE,sep = input$sep_msstatsptmdata, # fixed sep here

+      data = read.csv(input$msstatsptmdata$datapath, header = TRUE,sep = input$sep_msstatsptmdata, 

                       stringsAsFactors=FALSE)

       mydata = list("PTM" = data, "PROTEIN" = unmod)

     }

   }

   else if (input$filetype == "msstats"){

-    mydata = read.csv(input$msstatsdata$datapath, header = TRUE,sep = input$sep_msstatsdata, # fixed sep here

+    mydata = read.csv(input$msstatsdata$datapath, header = TRUE,sep = input$sep_msstatsdata, 

                       stringsAsFactors=FALSE)

   }

   else {

@@ -405,8 +404,8 @@ getData <- function(input) {

     #   }

     # }

-    if(input$filetype == '10col') {# this file not in use anymore, can delete?

-      mydata = read.csv(infile$datapath, header = TRUE, sep = input$sep_data) # not tested sep

+    if(input$filetype == '10col') {

+      mydata = read.csv(infile$datapath, header = TRUE, sep = input$sep_data) 

     }

     else if(input$filetype == 'sky') {

       cat(file=stderr(), "Reached here in skyline\n")

@@ -498,7 +497,6 @@ getData <- function(input) {

       #   data = read.csv.sql(infile$datapath, sep="\t",

       #                       sql = "select * from file order by random() limit 100000")

       # } else {

-      # data = read.csv(input$specdata$datapath, sep="\t")

       data = read.csv(input$specdata$datapath, sep=input$sep_specdata)

       # }

       mydata = SpectronauttoMSstatsFormat(data,

@@ -514,7 +512,6 @@ getData <- function(input) {

       #   data = read.csv.sql(infile$datapath, sep="\t",

       #                       sql = "select * from file order by random() limit 100000")

       # } else {

-      # data = read.csv(input$dianndata$datapath, sep="\t") # hard coded value here

       data = read.csv(input$dianndata$datapath, sep=input$sep_dianndata)

       # }

       print(input$dianndata$datapath)

@@ -583,7 +580,6 @@ getData <- function(input) {

       #   data = read.csv.sql(infile$datapath, sep = "\t",

       #                       sql = "select * from file order by random() limit 100000")

       # } else {

-      # data = read.csv(infile$datapath, sep="\t")

       data = read.csv(infile$datapath, sep=input$sep_data)

       # }

       mydata = SpectroMinetoMSstatsTMTFormat(data, getAnnot(input),