Hyungwon Choi

It seems that the data was properly run based on your list.txt file. There is a normalization step inside that scales the intensity value down in the final report (list.txt), and we replace zeros with a dot in the reporting. Unforunately the scoring algorithm must have determined that there is no significant interaction (all scores are zeros). I believe this has to do with the reproducibility across replicates. I'll look further to see if something else is wrong with the software.

Hi, which command line did you run? Was it SAINTexpress-int command? I just tried it and it ran OK. Also, you had a lot of places where you had "100" as the intensity. Are these imputed values? SAINTexpress can actually do imputation on its own, and I think you should try that instead of a plugged-in version. Usually we see a lot of missing data in the controls, but your data has no missing data at all -- which is unlikely from the raw data. Please feel free to contact me at email address: hwcho...

Hi, we will take a look and get back to you as soon as we figure it out. Hyungwon

Hi Craig, this is happening because there are interactions for which the intensities are all zero. It still tracks 0 intensities as missing observations within the software. We used to have a routine to plug zeros in, but at some point we decided not to do this for user's convenience.

Hi Craig, Can you try after removing all the interactions that has zero values? Hyungwon

I'm not too sure. Your data works on mine, both on mac and linux after removing the peptide column. The only thing I can suspect is the new line character difference, even then we addressed this issue in the code.

One thing I would do is to set "normalize_control=true" instead of false. Attaching the input and output again.

Not really, I just removed one column. I'm attaching the input and output files. Hw