#10 Error in Spec sum

[Robin Journot]

Hi,
First, thank you for this tool that is great.

I have a problem with one analysis where the column spectral sum, in the output failof Saintexpress contains mistakes.
Specsum should be the sum of spectral intensities as the data I have provided are intensities. When the intensities are too high (around 50 000), the sum is wrong.
Does the algorithm contains threshold for intensities level ?

Thank you for your help !

[Hyungwon Choi]

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

Hyungwon

[Robin Journot]

Thank you very much,

I forget to precise that I work with the SAINTexpress tool under galaxy at http://apostl.moffitt.org

Best regards,

Robin Journot

De: "Hyungwon Choi" hwchoi912@users.sourceforge.net
À: "[saint-apms:bugs]" 10@bugs.saint-apms.p.re.sourceforge.net
Envoyé: Mardi 17 Septembre 2019 13:41:27
Objet: [saint-apms:bugs] #10 Error in Spec sum

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

Hyungwon

[bugs:#10] Error in Spec sum

Status: open
Group: v1.0 (example)
Created: Tue Sep 17, 2019 12:19 AM UTC by Robin Journot
Last Updated: Tue Sep 17, 2019 12:19 AM UTC
Owner: nobody
Attachments:

* bait-wt.txt (65 Bytes; text/plain) 
* interaction-wt-intensity.txt (1.4 MB; text/plain) 
* prey-wt.txt (212.4 kB; text/plain)

Hi,
First, thank you for this tool that is great.

I have a problem with one analysis where the column spectral sum, in the output failof Saintexpress contains mistakes.
Specsum should be the sum of spectral intensities as the data I have provided are intensities. When the intensities are too high (around 50 000), the sum is wrong.
Does the algorithm contains threshold for intensities level ?

Thank you for your help !

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[Hyungwon Choi]

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: hwchoi@nus.edu.sg.