Problem with the export function Delphine Bachelet – 2013/01/16 Stepwise process on Austria data (2013_11_28)
Problem with the export function
Delphine Bachelet – 2013/01/16
Stepwise process on Austria data (2013_11_28)
Then…• I down-load the file clinical_i2b2trans.txt from Guest-DataExport1008
(see slide 4) onto my computer• I open it using R:
The example of the Treat variableR code:
> head(X$PATIENT.ID)
[1] "100" "1000" "10001" "10003" "10004" "10007"
> head(X$X.Biomarkers.Test.Treat.)
[1] "Rebif44; Rebif44; Betaferon" "Rebif44; Rebif; Rebif; Rebif44; Rebif" "Tysabri" "Rebif44; Rebif44; Rebif44" "Betaferon"
[6] "Tysabri"
Meaning that
Patient « 100 » had Rebif44 for visit 1, Rebif44 for visit 2, Betaferon for visit 3
Patient « 1000 » had Rebif44 for visit 1, Rebif for visit 2, Rebif for visit 3, Rebif44 for visit 4, Rebif for visit 5,
Patient « 10001 » had Tysabri for visit 1
Patient « 10003 » had Rebif44 for visit 1, Rebif44 for visit 2, Rebif44 for visit 3
Patient « 10004 » had Betaferon for visit 1
Patient « 10007 » had Tysabri for visit 1
But according to TranSMART…
Only one variable « Treat » for all the visits. Why that?
Patient ID R – visit 1 TranSMART – Visit 1
R – visit 2 TranSMART – Visit 2
R – visit 3 TranSMART – Visit 3
100 Rebif44 Betaferon Rebif44 Rebif44 Betaferon Rebif44
1000 Rebif44 Rebif Rebif Rebif Rebif Rebif
10001 Tysabri Tysabri
10003 Rebif44 Rebif44 Rebif44 Rebif44 Rebif44 Rebif44
10004 Betaferon Betaferon
10007 Tysabri Tysabri
Summary
…
…
Conclusion: The data from alphanumeric (categorical) variables of the exported file (clinical_i2b2trans.txt) are not correct and do not match with the data correctly displayed in the TranSMART grid view!