Hi Sandra, Tomas, Firstly thanks for the comments . As my file is some 15GB I don't think sending it to you is an option ;-) However I have played around with the data and by using the row filter I have filtered out peaks with fewer than 50 instances. This is probably where the program was struggling as I had a large number of peaks that only occurred rarely across the samples. After doing this the process ran in about 3 hours. Still slower than I would have expected but acceptable. Of course it is undesirable to filter in this way but for our particular study we are not looking for 'rarely occurring biomarkers' in the way you might for a medical application.
Regarding data analysis tools there are many mature products out there that can take data output from mzMine (SIMCA-P, MATLAB, OCTAVE, R etc.). I guess it's up to the community whether the program is dedicated for MS processing or if it evolves into a one-stop shop? Coming from a data analysis background my personal view is that it might open a can of worms that might divert resource away from developing the core MS functionality? (..it could be an endless source of arguments as to which methods work best!) One feature we are discussing here is an interface to R so that we can integrate some other ms processing tools into the workflows. As Weka is implemented in R then that might be a route to using it? My personal preference is for Chemometrics methods such as PCA, SIMCA and OPLS-DA. Certainly an easy port of data into R would make available a huge range of data analysis methods which are already available, without 're-inventing the wheel' The good news is we have had approval here to begin to contribute to the project, no doubt our developer Chris will be in touch soon with our proposals. Finally I can report that I have successfully processed my 218 run UPLC-MS study using mzmine. It has found some 3500 peaks and looking at the data using PCA we have some results consistent with earlier processing by other means. So thank you Thomas and other developers for a very useful and user friendly piece of software. Best regards, Mark -----Original Message----- From: mzmine-devel-requ...@lists.sourceforge.net [mailto:mzmine-devel-requ...@lists.sourceforge.net] Sent: 16 November 2010 01:16 To: mzmine-devel@lists.sourceforge.net Subject: Mzmine-devel Digest, Vol 30, Issue 9 Send Mzmine-devel mailing list submissions to mzmine-devel@lists.sourceforge.net 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 mzmine-devel-requ...@lists.sourceforge.net You can reach the person managing the list at mzmine-devel-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Mzmine-devel digest..." Today's Topics: 1. Re: Gap filling very slow (Castillo Sandra) 2. Weka library (Castillo Sandra) 3. Re: Weka library (Tomas Pluskal) 4. Gap filling very slow (mark.ea...@syngenta.com) 5. Re: Gap filling very slow (Tomas Pluskal) ---------------------------------------------------------------------- Message: 1 Date: Fri, 12 Nov 2010 09:53:41 +0200 From: Castillo Sandra <sandra.casti...@vtt.fi> Subject: Re: [Mzmine-devel] Gap filling very slow To: Developer discussion <mzmine-devel@lists.sourceforge.net> Message-ID: <94c37e6fd527c443b24ca58f2ccbc6c2d1729fa...@vttmail.ad.vtt.fi> Content-Type: text/plain; charset="us-ascii" Hi, are you using the option "retention time correction"? It could be the reason of the problem. With the retention time correction the gap filling module takes one sample randomly and fills all its gaps creating a model of the retention time shifts with the rest of the samples one by one. After that, this sample with the complete set of peaks is used to create the retention time model for all the other samples and fill the gaps. Any idea about how to improve it? Sandra ________________________________________ From: mark.ea...@syngenta.com [mark.ea...@syngenta.com] Sent: 11 November 2010 19:25 To: mzmine-devel@lists.sourceforge.net Subject: [Mzmine-devel] Gap filling very slow Dear Tomas, I am finding the gap filling algorithm very slow in mzmine. Its been running all day on my 210 samples and only 32% complete. Considering the RANSAC alignment only took 20 mins or so on the same data, this seems surprising. I would have though the RANSAC routine would be more computationally demanding than merely filling in empty rows? Perhaps this may be worth looking at in a future revision? Many thanks, Mark -- ----------------------------------------- Mark Earll Research Leader - Metabolomics Analytical Sciences (Office 102/65) [cid:image003.jpg@01CB81C5.81E24060] Jealott's Hill International Research Centre Bracknell Berkshire RG42 6EY United Kingdom Direct +44 1344 414316 mark.ea...@syngenta.com<mailto:firstname.surn...@syngenta.com> www.syngenta.com<http://www.syngenta.com/> ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ------------------------------ Message: 2 Date: Fri, 12 Nov 2010 10:03:43 +0200 From: Castillo Sandra <sandra.casti...@vtt.fi> Subject: [Mzmine-devel] Weka library To: Developer discussion <mzmine-devel@lists.sourceforge.net> Message-ID: <94c37e6fd527c443b24ca58f2ccbc6c2d1729fa...@vttmail.ad.vtt.fi> Content-Type: text/plain; charset="us-ascii" Hi, I have been playing with weka library these days. Do you think it would be useful to add data analysis algorithm for clustering or classification into MZmine? Cheers, Sandra ------------------------------ Message: 3 Date: Fri, 12 Nov 2010 17:30:43 +0900 From: Tomas Pluskal <plus...@oist.jp> Subject: Re: [Mzmine-devel] Weka library To: Developer discussion <mzmine-devel@lists.sourceforge.net> Message-ID: <9eb9b887-a72a-4715-9558-035354f11...@oist.jp> Content-Type: text/plain; charset=us-ascii Hi Sandra, I think that would be very useful, especially if you include nice visualization :) Tomas On Nov 12, 2010, at 5:03 PM, Castillo Sandra wrote: > Hi, > I have been playing with weka library these days. Do you think it would be > useful to add data analysis algorithm for clustering or classification into > MZmine? > Cheers, > Sandra > ------------------------------------------------------------------------------ > Centralized Desktop Delivery: Dell and VMware Reference Architecture > Simplifying enterprise desktop deployment and management using > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end > client virtualization framework. Read more! > http://p.sf.net/sfu/dell-eql-dev2dev > _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan TEL: +81-98-966-8684 ------------------------------ Message: 4 Date: Mon, 15 Nov 2010 11:04:15 +0100 From: <mark.ea...@syngenta.com> Subject: [Mzmine-devel] Gap filling very slow To: <mzmine-devel@lists.sourceforge.net> Message-ID: <062dc6c03141da48bbcc1b5a02d0d5a4060ed15...@frgocmsxmb04.eame.syngenta.org> Content-Type: text/plain; charset="us-ascii" Hi Tomas, I have left my PC running for 4 days and the gap filling is still only 48% complete. Since it was only 32% complete after one day it seems to be getting slower with time. Is there any reason this is so computationally intensive or is there a bug? Many thanks, Mark -- ----------------------------------------- Mark Earll Research Leader - Metabolomics Analytical Sciences (Office 102/65) [cid:image001.jpg@01CB84AC.76015030] Jealott's Hill International Research Centre Bracknell Berkshire RG42 6EY United Kingdom Direct +44 1344 414316 mark.ea...@syngenta.com<mailto:firstname.surn...@syngenta.com> www.syngenta.com<http://www.syngenta.com/> message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. -------------- next part -------------- An HTML attachment was scrubbed... -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 1567 bytes Desc: image001.jpg ------------------------------ Message: 5 Date: Tue, 16 Nov 2010 10:15:34 +0900 From: Tomas Pluskal <plus...@oist.jp> Subject: Re: [Mzmine-devel] Gap filling very slow To: Developer discussion <mzmine-devel@lists.sourceforge.net> Message-ID: <161aa1ab-b420-4d77-969b-61b14c137...@oist.jp> Content-Type: text/plain; charset="us-ascii" Hi Mark, There is nothing we can do with reports like the one you wrote. Gap filling works fine with our data. If you send us your MZmine project file and the exact parameters which you used for gap filling, we can take a look at it and find why it is slow. Or you can ask your engineers to take a look at it, as a first contribution to MZmine :) By the way, did you see Sandra's message? Best regards, Tomas On Nov 15, 2010, at 7:04 PM, <mark.ea...@syngenta.com> <mark.ea...@syngenta.com> wrote: > Hi Tomas, > > I have left my PC running for 4 days and the gap filling is still only 48% > complete. Since it was only 32% complete after one day it seems to be getting > slower with time. > > Is there any reason this is so computationally intensive or is there a bug? > > Many thanks, > > Mark > > -- ----------------------------------------- > Mark Earll > Research Leader - Metabolomics > Analytical Sciences (Office 102/65) > > <image001.jpg> > > Jealott's Hill International Research Centre > Bracknell > Berkshire > RG42 6EY > United Kingdom > Direct +44 1344 414316 > mark.ea...@syngenta.com > www.syngenta.com > > > > This message may contain confidential information. If you are not the > designated recipient, please notify the sender immediately, and delete the > original and any copies. Any use of the message by you is prohibited. > ------------------------------------------------------------------------------ > Centralized Desktop Delivery: Dell and VMware Reference Architecture > Simplifying enterprise desktop deployment and management using > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end > client virtualization framework. Read more! > http://p.sf.net/sfu/dell-eql-dev2dev_______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan TEL: +81-98-966-8684 -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ------------------------------ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel End of Mzmine-devel Digest, Vol 30, Issue 9 ******************************************* message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. 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