Hi Tomas,
I'm not sure, but I believe this would not change that much my workflow
neither the nature of the results, since we are working on GC/MS data
and usually not using bins bigger than 1, neither any other parameter
from the "Chromatogram Builder" altering/filtering the signal (like "Min
Intensity", ...). My goal being only to reduce the number of detected
peaks "after" deconvolution. In this same point of view, I am working on
a module which aims to filter the peaks from the deconvoluted list on
the basis of their shape (that is to say, removing peaks that do not
have the shape of a peak, inspired by the "Shaper" module). Probably
combining this shape approach with some other restrictions like minimum
top/edges ratio...
At least, this will be my next concern once I am satisfied with the
baseline feature (hopefully soon).
To answer your question, performing the baseline on detected
chromatograms only would certainly reduce the duration of the baselining
task for some use cases, but not in mine, because I do not use the
"Chromatogram Builder" to skip or merge anything in the "m/z dimension".
I only use it to split every single m/z slice. Then I apply
deconvolution and finally merge the pieces that share the same user
defined "RT tolerance" range using a module named "RT based peaks
merger" (which, by the way, is not completely satisfying in the way it
is implemented at this time).
Best
Gauthier
On 11/14/2014 10:34 AM, Tomas Pluskal wrote:
Hi Gauthier, Chris,
I was wondering about your typical usage pattern of the baseline
correction module. Since the baseline correction algorithms take
chromatograms as an input, wouldn't it make more sense to perform it
after running the Chromatogram builder?
Chris, could you remind me what was the motivation to implement
baseline correction on the raw data with m/z binning, instead of doing
it on detected chromatograms?
Best regards,
Tomas
===============================================
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
------------------------------------------------------------------------------
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
--
Gauthier BOAGLIO
CEFE - UMR 5175
1919 route de Mende
F-34293 Montpellier cedex 5
Tel: +33/0 4 67 61 32 15
Fax: +33/0 4 67 61 33 36
email: gauthier.boag...@cefe.cnrs.fr
www:
http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio
http://www.evolepid.org/people.php?name=boaglio
------------------------------------------------------------------------------
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
