Hi, is the deviation in the retention time linear? The parameters seem reasonable. Could you send me 2 samples so I can try the alignment myself and I can see what is the problem? Try to put the Min no of points very low (like 1%) and see if it improves. If you have so many peaks, and the RT window is big, there are many possible alignments, and the number of points inside the model compared with the number of possibilities is very low. BR, Sandra ________________________________________ From: Raghavendra Gunnaiah [raghavendra.gunna...@mail.mcgill.ca] Sent: 16 July 2012 22:47 To: mzmine-devel@lists.sourceforge.net Subject: [Mzmine-devel] RANSAC alignment
Dear Developers, Greetings! To align 20 samples, I used following parameters in RANSAC m/z tolerance=0.02 or 25 ppm RT tolerance=1.5 min RT tolerance after correction= 1.00 min RANSAC iterations= 2000 Min no of points 30% Threshold value= 0.03 (I also tried upto 0.5) After alignment, I do see lot of aligned pairs, with threshold value=0.5, I see all aligned pairs in the preview. But when I look at the table of aligned peaks, I don't see proper alignment. Single peak is considered more than 3-4 times with different samples. For example, on average I got 4000 peaks/sample after deconvolution, while I see more than 30,000 peaks in the alignment table. I didn't understand exactly what is threshold value. Can you please suggest me the optimum parameters for RANSAC alignment . Maximum RT deviation observed in my samples is less than one min. With kind regards Raghavendra Gunnaiah Ph.D. scholar Department of Plant Science McGill Univerisity, Canada ------------------------------------------------------------------------------ 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 Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel ------------------------------------------------------------------------------ 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 Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
