{"action":"created","issue":{"url":"https://api.github.com/repos/rietho/IPO/issues/43","repository_url":"https://api.github.com/repos/rietho/IPO","labels_url":"https://api.github.com/repos/rietho/IPO/issues/43/labels{/name}","comments_url":"https://api.github.com/repos/rietho/IPO/issues/43/comments","events_url":"https://api.github.com/repos/rietho/IPO/issues/43/events","html_url":"https://github.com/rietho/IPO/issues/43","id":190312932,"number":43,"title":"Error in .local(object, ...) :    Dimensions of profile matrices do not match !","user":{"login":"mheiser-md","id":13658867,"avatar_url":"https://avatars.githubusercontent.com/u/13658867?v=3","gravatar_id":"","url":"https://api.github.com/users/mheiser-md","html_url":"https://github.com/mheiser-md","followers_url":"https://api.github.com/users/mheiser-md/followers","following_url":"https://api.github.com/users/mheiser-md/following{/other_user}","gists_url":"https://api.github.com/users/mheiser-md/gists{/gist_id}","starred_url":"https://api.github.com/users/mheiser-md/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mheiser-md/subscriptions","organizations_url":"https://api.github.com/users/mheiser-md/orgs","repos_url":"https://api.github.com/users/mheiser-md/repos","events_url":"https://api.github.com/users/mheiser-md/events{/privacy}","received_events_url":"https://api.github.com/users/mheiser-md/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-11-18T12:55:11Z","updated_at":"2016-11-18T13:32:04Z","closed_at":null,"body":"For a while now I've come across the following error message when running _optimizeRetGroup_ in single core mode:\r\n\r\n```\r\nError in .local(object, ...) : \r\n  Dimensions of profile matrices do not match !\r\n```\r\n\r\nI ignored for a while, up until my data processing pipeline crashed during the retcor.obiwarp step with the above message using optimized IPO parameters. \r\nOnce I reran IPO in single core mode, I could see the message was being printed for every sample, which seems to be a rare case? \r\n\r\nWith the following script the error can be reproduced:\r\n\r\n```r\r\nlibrary(msdata)\r\nlibrary(IPO)\r\nlibrary(xcms)\r\n\r\nmzdatapath <- system.file(\"mzData\", package = \"mtbls2\")\r\nmzdatafiles <- list.files(mzdatapath, recursive = TRUE, full.names=TRUE)\r\n\r\nxset <- xcmsSet(\r\n  mzdatafiles[1:12],  method = \"centWave\",  peakwidth = c(6.65, 25), ppm = 25, \r\n  mzdiff = -0.001, snthresh = 10, noise = 10000, prefilter = c(3, 100), nSlaves = 3\r\n)\r\n\r\nparamsRG <- getDefaultRetGroupStartingParams()\r\n\r\nresultRG <- optimizeRetGroup(xset, paramsRG, nSlaves=1)\r\n```\r\n\r\nAnd this is the output: The retcor step seems to stop after sample MSpos-Ex1-cyp79-48h-Ag-1_1-B,1_01_9819 in every iteration. \r\n```\r\nstarting new DoE with:\r\n\r\ndistFunc: cor_opt\r\ngapInit: c(0, 0.4)\r\ngapExtend: c(2.1, 2.7)\r\nprofStep: c(0.7, 1)\r\nplottype: none\r\nresponse: 1\r\nfactorDiag: 2\r\nfactorGap: 1\r\nlocalAlignment: 0\r\nretcorMethod: obiwarp\r\nbw: c(22, 38)\r\nminfrac: c(0.3, 0.7)\r\nmzwid: c(0.015, 0.035)\r\nminsamp: 1\r\nmax: 50\r\ncenter: 10\r\n\r\ncenter sample:  MSpos-Ex2-Col0-48h-Ag-2_1-A,3_01_9829 \r\nProcessing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820  MSpos-Ex1-Col0-48h-Ag-3_1-A,1_01_9822  MSpos-Ex1-Col0-48h-Ag-4_1-A,1_01_9824  MSpos-Ex1-cyp79-48h-Ag-1_1-B,1_01_9819  \r\nError in .local(object, ...) : \r\n  Dimensions of profile matrices do not match !\r\n\r\n108 112 115 119 123 127 130 134 138 142 145 149 153 157 160 164 168 172 175 179 183 187 190 194 198 202 205 209 213 217 220 224 228 232 235 239 243 247 250 254 258 262 265 269 273 277 280 284 288 292 295 299 303 307 310 314 318 322 325 329 333 337 340 344 348 352 355 359 363 367 370 374 378 382 385 389 393 397 400 404 408 412 415 419 423 427 430 434 438 442 445 449 453 457 460 464 468 472 475 479 483 487 490 494 498 502 505 509 513 517 520 524 528 532 535 539 543 547 550 554 558 562 565 569 573 577 580 584 588 592 595 599 603 607 610 614 618 622 625 629 633 637 640 644 648 652 655 659 663 667 670 674 678 682 685 689 693 697 700 704 708 712 715 719 723 727 730 734 738 742 745 749 753 757 760 764 768 772 775 779 783 787 790 794 798 802 805 809 813 817 820 824 828 832 835 839 843 847 850 854 858 862 865 869 \r\ncenter sample:  MSpos-Ex2-Col0-48h-Ag-2_1-A,3_01_9829 \r\nProcessing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820  MSpos-Ex1-Col0-48h-Ag-3_1-A,1_01_9822  MSpos-Ex1-Col0-48h-Ag-4_1-A,1_01_9824  MSpos-Ex1-cyp79-48h-Ag-1_1-B,1_01_9819  \r\nError in .local(object, ...) : \r\n  Dimensions of profile matrices do not match !\r\n\r\n108 112 115 119 123 127 130 134 138 142 145 149 153 157 160 164 168 172 175 179 183 187 190 194 198 202 205 209 213 217 220 224 228 232 235 239 243 247 250 254 258 262 265 269 273 277 280 284 288 292 295 299 303 307 310 314 318 322 325 329 333 337 340 344 348 352 355 359 363 367 370 374 378 382 385 389 393 397 400 404 408 412 415 419 423 427 430 434 438 442 445 449 453 457 460 464 468 472 475 479 483 487 490 494 498 502 505 509 513 517 520 524 528 532 535 539 543 547 550 554 558 562 565 569 573 577 580 584 588 592 595 599 603 607 610 614 618 622 625 629 633 637 640 644 648 652 655 659 663 667 670 674 678 682 685 689 693 697 700 704 708 712 715 719 723 727 730 734 738 742 745 749 753 757 760 764 768 772 775 779 783 787 790 794 798 802 805 809 813 817 820 824 828 832 835 839 843 847 850 854 858 862 865 869 \r\ncenter sample:  MSpos-Ex2-Col0-48h-Ag-2_1-A,3_01_9829 \r\nProcessing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820  MSpos-Ex1-Col0-48h-Ag-3_1-A,1_01_9822  MSpos-Ex1-Col0-48h-Ag-4_1-A,1_01_9824  MSpos-Ex1-cyp79-48h-Ag-1_1-B,1_01_9819  \r\nError in .local(object, ...) : \r\n  Dimensions of profile matrices do not match !\r\n```\r\n\r\nIt looks to me like a xcms bug, but I was wondering if IPO can perform any retcor optimization with this error?"},"comment":{"url":"https://api.github.com/repos/rietho/IPO/issues/comments/261532101","html_url":"https://github.com/rietho/IPO/issues/43#issuecomment-261532101","issue_url":"https://api.github.com/repos/rietho/IPO/issues/43","id":261532101,"user":{"login":"jotsetung","id":5506112,"avatar_url":"https://avatars.githubusercontent.com/u/5506112?v=3","gravatar_id":"","url":"https://api.github.com/users/jotsetung","html_url":"https://github.com/jotsetung","followers_url":"https://api.github.com/users/jotsetung/followers","following_url":"https://api.github.com/users/jotsetung/following{/other_user}","gists_url":"https://api.github.com/users/jotsetung/gists{/gist_id}","starred_url":"https://api.github.com/users/jotsetung/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jotsetung/subscriptions","organizations_url":"https://api.github.com/users/jotsetung/orgs","repos_url":"https://api.github.com/users/jotsetung/repos","events_url":"https://api.github.com/users/jotsetung/events{/privacy}","received_events_url":"https://api.github.com/users/jotsetung/received_events","type":"User","site_admin":false},"created_at":"2016-11-18T13:32:04Z","updated_at":"2016-11-18T13:32:04Z","body":"OK, the error comes from the `retcor.obiwarp`. I'll have to look into this - but am pretty busy at the moment - this might take some time."}}
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