Hello I have a question about TPP analysis by using the data searched by Proteome Discoverer. I prepared my configuration table and other data tables following the instruction provided by Franken et al. 2014 (doi:10.1038/nprot.2015.101). However I see the below error when I try to import the data and start the analysis. I will be grateful if someone can advice me on this error.

> TRresults <- analyzeTPPTR(configTable = myConfigTable,methods = "meltcurvefit",data = my_TPP-TR_Data)
This is TPP version 3.14.1.
Importing data...
Error in is.data.frame(infoTable) : object 'myConfigTable' not found

Thanks

The error states that there is no object in your workspace by the name of myConfigTable; so, you must first create that object. The manual entry for this object states:

dataframe, or character object with the path to a file, that specifies important details of the TPP-TR experiment. See Section details for instructions how to create this object.

To see an example, load the sample data:

require(TPP)

data(hdacTR_smallExample)

hdacTR_config
      Experiment Condition ComparisonVT1 ComparisonVT2 126 127L 127H 128L 128H
1      Vehicle_1   Vehicle             x                67   63   59   56   53
2      Vehicle_2   Vehicle                           x  67   63   59   56   53
3 Panobinostat_1 Treatment             x                67   63   59   56   53
4 Panobinostat_2 Treatment                           x  67   63   59   56   53
  129L 129H 130L 130H 131L
1   50   47   44   41   37
2   50   47   44   41   37
3   50   47   44   41   37
4   50   47   44   41   37

tpptrResults <- analyzeTPPTR(configTable=hdacTR_config, data=hdacTR_data, nCores=1)

If you would like further help with this, then please add more information about the exact source of the data that you have obtained, and also including all commands prior to the one that you have posted in your question.

Kevin