Hello Joe,
Sorry for responding with half-year delay, but only now I have some time to
return back to MZmine development. You were right about the bug, it is
surprising that nobody noticed this before.
I think the meaning of the m/z and RT weight parameters is not so clear, so in
the future I would like to update the algorithm, to reduce the number of
parameters. But for now, I just fixed the usage of m/z weight. This change will
be included in the new MZmine release, hopefully coming soon.
Best regards,
Tomas
On Jan 5, 2014, at 6:13, Joe Wandy
<10067...@student.gla.ac.uk<mailto:10067...@student.gla.ac.uk>> wrote:
Hi MZMine developers,
Happy holidays !
I was checking how the Join aligner works, and noticed that inside the
class
net.sf.mzmine.modules.peaklistmethods.alignment.join.JoinAlignerTask,
the instance variable mzWeight is never initialised in the constructor.
As a result, when computing the score for alignment of rows inside
RowVsRowScore, the contribution of m/z difference to the score is always
0. So, only the RT difference is used for score calculation at the
moment, despite the fact that on the GUI, we can specify the weights to
both m/z and RT.
It seems like a bug to me ? If I'm wrong, please let me know. Thanks !
Joe
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Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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