Skip to main content
Topic: How to export alignment result in mztab-M format (Read 363 times) previous topic - next topic

How to export alignment result in mztab-M format

With recent versions of MSDIAL, I see there is an option to export data in mztab-M format. We would like to use this format but when I try to export alignment data using this option (while no other options are selected), no file gets generated. If there is another option selected (such as Normalized data matrix) in addition to mztab-M option, an error is displayed and MSDIAL crashes.
Is there any solution to this?
Thank you,
Vladimir.

 

Re: How to export alignment result in mztab-M format

Reply #1
Hi Vladimir,

The mzTab-M export will only work if you have (A)  'aligned' the data, and from the alignment option, and (B) when choosen with the corresponding text file export for either height/ areas, and not for mzTab-M exclusively etc. PLUS, importantly, either "Area" or "Height" has to be chosen besides the "mzTab-M" option, as it will export them in pairs,i.e., .text version of height/ area alongside the mzTab-M version of height/ area. So, at least 2 checks.

I do not face such issue with mzTab-M export at least in the current versions or 1-2 versions earlier.

If you have NOT normalized the data after alignment is done, then checking 'Normalized data' option will result in a crash/non-export etc. So prior to exporting data as :"Normalized data matrix" the data needs to be normalized while you are on the "aligned results" tab on your (left) hand side panel/bars.

Check out the 2 attached figs and see if those help too!

Thanks,
Biswa

Re: How to export alignment result in mztab-M format

Reply #2
Thanks Biswa, you are right.
I will fix the clash issue to let users know how the check/uncheck option works for generating mztab-M format.
Thanks,

Hiroshi

Re: How to export alignment result in mztab-M format

Reply #3
Thank you Biswa and Hiroshi for your comments. I gave it another try today but I am getting the same error with the latest version of MSDIAL. I select mztab-M option in addition to the raw area data and the error appears and then MSDIAL crashes. The same happens when combining with a normalized data export (while making sure the data is normalized). Please see the screenshot of the error. Are there any other parameters prior to exporting that need to be correct for this to work?
Thank you,
Vladimir.

Re: How to export alignment result in mztab-M format

Reply #4
We will fix this update. Instead, can you export mztab-m with "raw data matrix (height)"?

Hiroshi

Re: How to export alignment result in mztab-M format

Reply #5
Thank you Hiroshi. The error is the same if I select raw heights as an output combined with mztab-M. If this could be looked into for the next version it would be great.
Thank you,
Vladimir.