#9 SAINTexpress-int Aborted

[Craig Lawless]

Hi, I'm using SAINTexpress using intensity data and I'm getting an aborted (core dumped) error with one of our experiments.

Using the program as follows with the attached files:
SAINTexpress-int INTER_RAB25.txt PREY_RAB25.txt BAIT_RAB25.txt

I get:
terminate called after throwing an instance of 'char const'
Aborted (core dumped)

With no other explanation. I have checked the files and there are no errors with the files from what I can see.

Any help greatly appreciated.

Regards
Craig

[Hyungwon Choi]

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

[Craig Lawless]

Hi Hyungwon,

It works with all interactions with zero intensity removed.

So does SAINTexpress not treat zero intensity interactions the same as those that are missing (from control/IP replicates)?

Thank you

Craig

[Hyungwon Choi]

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.

[rachita srivastava]

[Jonathan Boulais]

Hi Hyungwon,

I'm using SAINTexpress-int on intensity data. While I removed proteins having zero intensities, I'm getting a termination similar to Craig's :

terminate called after throwing an instance of 'char const*'
Aborted

As a test, I ran SAINTexpress-spc using the same files and it works fine.

Any help would be appreciated !

Many thanks !

Jonathan