Hi Martin, I too wanted to be able to add together scans, or even better subtract one from another. This would have been a good way to remove background peaks by subtracting blank runs for example.
However when you sit down and think about this it becomes very problematic for accurate mass data. We even attempted to do this but the resultant chromatograms were awful because the slight variation in mass meant there was effectively missing data in some parts of the scan. We thought long and hard about this, I think the only way to do this would be to re-sample the data onto a common grid and then align the peaks before subtraction. We realised that this would result in quite a radical re-engineering of MZmine so we abandoned the idea as it was taking too much of our resources and there were other more important areas to focus on like peak picking. Cheers, Mark -- ----------------------------------------- Mark Earll Research Leader - Metabolomics Syngenta Jealott's Hill International Research Centre Bracknell Berkshire RG42 6EY United Kingdom -----Original Message----- From: [email protected] [mailto:[email protected]] Sent: 22 October 2012 11:54 To: [email protected] Subject: Mzmine-devel Digest, Vol 53, Issue 6 Send Mzmine-devel mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/mzmine-devel or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of Mzmine-devel digest..." Today's Topics: 1. Re: Is there a way to export "raw" files? (Martin Lewitt) 2. grouping of samples (gegoe) 3. Re: is there a scan summing or stacking method? (Geert Goeminne) ---------------------------------------------------------------------- Message: 1 Date: Sun, 14 Oct 2012 22:35:32 -0600 From: Martin Lewitt <[email protected]> Subject: Re: [Mzmine-devel] Is there a way to export "raw" files? To: Developer discussion <[email protected]> Message-ID: <CAHd=Pt3Rnj_tsQ0kNyNFN_wjqMAbrHUaWymnuUxhW=b8afv...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Thanx, I wasn't going to involve R, I just figured that baselining was an example of where you were exporting the same data I'll be dealing with. Thanx for the pointer. -- Martin On Sun, Oct 14, 2012 at 9:37 PM, Tomas Pluskal <[email protected]> wrote: > Hi Martin, > > I don't see the reason why R should be involved here. The easiest way > is just to write a new java module that takes the raw data using the > existing interface and writes a minimalistic mzML or mzXML file. > > E.g. take a look at the Scan.getDataPoints() method: > http://sourceforge.net/p/mzmine/code/3244/tree/trunk/src/main/java/net > /sf/mzmine/data/Scan.java > > Tomas > > > > On Oct 15, 2012, at 12:18 PM, Martin Lewitt > <[email protected]> > wrote: > > Where would you do it? My inclination is to model it on where you > pass the data to R. Everything has to be there I would think. Of > course, I would put in in the proper place in the raw input/(export) menu. > > thanx, > Martin > > On Sun, Oct 14, 2012 at 6:37 PM, Tomas Pluskal <[email protected]> wrote: > >> Hi Martin, >> >> MZmine currently does not have a module to export RAW data. >> Implementation of such module would not be difficult, though. If you >> want to work on that, I can assist you. >> >> Best regards, >> >> Tomas >> >> >> On Oct 12, 2012, at 9:32 PM, Martin Lewitt >> <[email protected]> >> wrote: >> >> mzmine-devel, >> >> I don't see a way to export "raw" files under the raw files menu. >> It would be helpful to be able to export intermediate results that >> get stored as raw files for evaluation or processing by other >> software. If the facility doesn't exist would it be easy to >> implement? I envision retaining the scan structure in an XML or >> mzXML format, and a possible stretch goal of being able to export just >> selected scans. >> >> regards, >> Martin Lewitt >> [email protected] >> >> --------------------------------------------------------------------- >> --------- Don't let slow site performance ruin your business. Deploy >> New Relic APM Deploy New Relic app performance management and know >> exactly what is happening inside your Ruby, Python, PHP, Java, and >> .NET app Try New Relic at no cost today and get our sweet Data Nerd >> shirt too! >> >> http://p.sf.net/sfu/newrelic-dev2dev_________________________________ >> ______________ >> Mzmine-devel mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/mzmine-devel >> >> >> =============================================== >> Tom?? 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 >> >> > ---------------------------------------------------------------------- > -------- Don't let slow site performance ruin your business. Deploy > New Relic APM Deploy New Relic app performance management and know > exactly what is happening inside your Ruby, Python, PHP, Java, and > .NET app Try New Relic at no cost today and get our sweet Data Nerd > shirt too! > > http://p.sf.net/sfu/newrelic-dev2dev__________________________________ > _____________ > Mzmine-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > > > =============================================== > Tom?? 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 > > > > ---------------------------------------------------------------------- > -------- Don't let slow site performance ruin your business. Deploy > New Relic APM Deploy New Relic app performance management and know > exactly what is happening inside your Ruby, Python, PHP, Java, and > .NET app Try New Relic at no cost today and get our sweet Data Nerd > shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > _______________________________________________ > Mzmine-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > > -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 2 Date: Mon, 22 Oct 2012 03:17:24 -0700 (PDT) From: gegoe <[email protected]> Subject: [Mzmine-devel] grouping of samples To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=us-ascii Hi, I know in Mzmine you can add extra parameters to the samples, like a group number, but how do you get this group number in the table after processing data? I want to be able to filter my results based on the groupnumber, or order them by groupnumber, but i can't find a way to get that groupnumber make appear in my table, anyone any idea how to do that? In the table properties you can not find that extra paramter, how come? Thanks for the replies, Cheers, Geert -- View this message in context: http://mzmine-devel-developer-discussion.970458.n3.nabble.com/grouping-of-samples-tp4024102.html Sent from the Mzmine-devel -- Developer discussion mailing list archive at Nabble.com. ------------------------------ Message: 3 Date: Mon, 22 Oct 2012 12:29:18 +0200 (CEST) From: "Geert Goeminne" <[email protected]> Subject: Re: [Mzmine-devel] is there a scan summing or stacking method? To: Developer discussion <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Hi, I know in Mzmine you can add extra parameters to the samples, like a group number, but how do you get this group number in the table after processing data? I want to be able to filter my results based on the groupnumber , or order them by groupnumber , but i can't find a way to get that groupnumber make appear in my table, anyone any idea how to do that? In the table properties you can not find that extra paramter, how come? Thanks for the replies, Cheers, Geert ----- Original Message ----- > From: "Tomas Pluskal" <[email protected]> > To: "Developer discussion" <[email protected]> > Sent: Friday, August 31, 2012 9:00:19 AM > Subject: Re: [Mzmine-devel] is there a scan summing or stacking > method? > Hi Martin, > We currently don't have such method, although it would not be > difficult to add it. > If you send me a detailed description of how such algorithm should > work, I can implement it. > Best regards, > Tomas > On Aug 31, 2012, at 3:46 AM, Martin Lewitt < > [email protected] > wrote: > > mzmine-devel, > > > I am a new user of MZmine 2. After selecting a set of raw scans > > using the crop method, I would like to be able to sum them together > > before further processing. I don't see a method to do this. I'm not > > familiar with the UI organization. Have I missed such a method? > > > regards and thanx for any assistance, > > > Martin Lewitt > > > [email protected] > > -------------------------------------------------------------------- > > ---------- > > > Live Security Virtual Conference > > > Exclusive live event will cover all the ways today's security and > > > threat landscape has changed and how IT managers can respond. > > Discussions > > > will include endpoint security, mobile security and the latest in > > malware > > > threats. > > http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___________ > > ____________________________________ > > > Mzmine-devel mailing list > > > [email protected] > > > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > > =============================================== > Tom?? 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 > ---------------------------------------------------------------------- > -------- > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest in > malware threats. > http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Mzmine-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mzmine-devel -- ================================================================== Geert Goeminne, Ing. Tel:+32 (0)9 331 38 37 or (0)9 331 38 79 fax:+32 (0)9 331 38 09 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM [email protected] http://www.psb.vib-ugent.be ================================================================== -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ------------------------------ _______________________________________________ Mzmine-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mzmine-devel End of Mzmine-devel Digest, Vol 53, Issue 6 ******************************************* This message may contain confidential information. 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