Unable to determine between-run-interference score

[Chris Soon Heng Tan]

Hi all

I have DIA data for 36 proteins output from Skyline. I am able to use "dataProcess" to processed the data but I run into problem whenever I set the parameter "betweenRunInterferenceScore" =TRUE. The error output is as below. What could contribute to this error?

** There are 196 intensities which are zero or less than 1. These intensities are replaced with 1.
Error in data.frame(names[, c("PROTEIN", "PEPTIDE", "FEATURE")], BetweenRunInterferenceScore = temp4) :
  arguments imply differing number of rows: 1018, 991


Many thanks

Chris Tan