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rietho / IPO

A Tool for automated Optimization of XCMS Parameters
http://bioconductor.org/packages/IPO/
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IPO optimized parameter showed peak data insertion problem #56

Open Titan100 opened 6 years ago

Titan100 commented 6 years ago

Hi @rietho and @sneumann , I optimized xcms parameters using QC files (40 files) that represented run across the 1000 samples. I used the optimized parameters to preprocess data using xcms and got peak data insertion problems (a part of run shown below). The data are centroided using MSConvert. I think I cannot get get rid or this issue whatever low ppm I set as the sample number is large(?). What would be your suggestion? Is it okay to ignore the warnings? ` Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 669 peak data insertion problems. Please try lowering the "ppm" parameter.

26652 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 12860 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 575 peak data insertion problems. Please try lowering the "ppm" parameter.

26954 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 12848 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 538 peak data insertion problems. Please try lowering the "ppm" parameter.

27709 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 13675 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 1199 peak data insertion problems. Please try lowering the "ppm" parameter.

28132 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 13862 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 374 peak data insertion problems. Please try lowering the "ppm" parameter.

29426 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 14561 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 26404 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 12199 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 1294 peak data insertion problems. Please try lowering the "ppm" parameter.

28456 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 13881 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 544 peak data insertion problems. Please try lowering the "ppm" parameter.

28764 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 14503 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 777 peak data insertion problems. Please try lowering the "ppm" parameter.

27160 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 12980 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 28058 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 13824 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 940 peak data insertion problems. Please try lowering the "ppm" parameter.

26626 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 12938 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 972 peak data insertion problems. Please try lowering the "ppm" parameter.

27253 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 13433 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 1104 peak data insertion problems. Please try lowering the "ppm" parameter.

28248 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 14274 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 422 peak data insertion problems. Please try lowering the "ppm" parameter.

28472 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 13928 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 813 peak data insertion problems. Please try lowering the "ppm" parameter.

29456 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 14769 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 478 peak data insertion problems. Please try lowering the "ppm" parameter.

28726 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 14098 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 425 peak data insertion problems. Please try lowering the "ppm" parameter.

28088 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 13956 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 1589 peak data insertion problems. Please try lowering the "ppm" parameter.

29614 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 14926 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 457 peak data insertion problems. Please try lowering the "ppm" parameter.

26932 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 12673 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 1191 peak data insertion problems. Please try lowering the "ppm" parameter.

28600 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 14367 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 287 peak data insertion problems. Please try lowering the "ppm" parameter.

28274 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 13824 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 146 peak data insertion problems. Please try lowering the "ppm" parameter.

29337 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 14916 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 954 peak data insertion problems. Please try lowering the "ppm" parameter.

29853 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 15198 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 424 peak data insertion problems. Please try lowering the "ppm" parameteLoading required package: xcms Loading required package: mzR Loading required package: Rcpp Loading required package: BiocGenerics Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

IQR, mad, xtabs

The following objects are masked from 'package:base':

anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min

Loading required package: ProtGenerics Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 265 peak data insertion problems. Please try lowering the "ppm" parameter.

32554 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17989 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 809 peak data insertion problems. Please try lowering the "ppm" parameter.

31295 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 16861 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 31840 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17597 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 30567 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 16131 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 78 peak data insertion problems. Please try lowering the "ppm" parameter.

31658 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17181 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 67 peak data insertion problems. Please try lowering the "ppm" parameter.

31790 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 16993 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 273 peak data insertion problems. Please try lowering the "ppm" parameter.

32591 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17360 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 750 peak data insertion problems. Please try lowering the "ppm" parameter.

32899 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17315 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 66 peak data insertion problems. Please try lowering the "ppm" parameter.

34151 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 18388 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 33546 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17717 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 352 peak data insertion problems. Please try lowering the "ppm" parameter.

32329 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17192 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 33783 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 18269 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 154 peak data insertion problems. Please try lowering the "ppm" parameter.

33049 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17765 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 352 peak data insertion problems. Please try lowering the "ppm" parameter.

32448 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17120 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 188 peak data insertion problems. Please try lowering the "ppm" parameter.

32609 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17848 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 945 peak data insertion problems. Please try lowering the "ppm" parameter.

33956 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 18135 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 8 peak data insertion problems. Please try lowering the "ppm" parameter.

34329 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 18286 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 33393 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17781 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 51 peak data insertion problems. Please try lowering the "ppm" parameter.

32928 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17846 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 6 peak data insertion problems. Please try lowering the "ppm" parameter.

32837 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 16831 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 718 peak data insertion problems. Please try lowering the "ppm" parameter.

32474 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17699 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 74 peak data insertion problems. Please try lowering the "ppm" parameter.

32047 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17414 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 6 peak data insertion problems. Please try lowering the "ppm" parameter.

31945 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 17637 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 33 peak data insertion problems. Please try lowering the "ppm" parameter.

33710 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 18598 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 818 peak data insertion problems. Please try lowering the "ppm" parameter.

Loading required package: xcms Loading required package: mzR Loading required package: Rcpp Loading required package: BiocGenerics Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

IQR, mad, xtabs

The following objects are masked from 'package:base':

anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min

Loading required package: ProtGenerics Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 35121 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 18643 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 266 peak data insertion problems. Please try lowering the "ppm" parameter.

35212 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 19042 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 35798 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 19372 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 29 peak data insertion problems. Please try lowering the "ppm" parameter.

35169 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 19113 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 35202 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 18967 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 38150 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20627 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 1139 peak data insertion problems. Please try lowering the "ppm" parameter.

38425 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20924 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 60 peak data insertion problems. Please try lowering the "ppm" parameter.

38724 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20900 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 143 peak data insertion problems. Please try lowering the "ppm" parameter.

38632 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 21135 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 36409 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 19626 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 314 peak data insertion problems. Please try lowering the "ppm" parameter.

38776 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 21531 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 38394 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20618 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 257 peak data insertion problems. Please try lowering the "ppm" parameter.

39106 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 21229 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 38638 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20823 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 476 peak data insertion problems. Please try lowering the "ppm" parameter.

38415 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20793 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 222 peak data insertion problems. Please try lowering the "ppm" parameter.

38933 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 21288 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 251 peak data insertion problems. Please try lowering the "ppm" parameter.

37633 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20239 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 134 peak data insertion problems. Please try lowering the "ppm" parameter.

36524 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20162 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 19076 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 7301 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 40 peak data insertion problems. Please try lowering the "ppm" parameter.

36699 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 19976 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 37232 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20458 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 40271 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 21700 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 10 peak data insertion problems. Please try lowering the "ppm" parameter.

38370 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20765 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 309 peak data insertion problems. Please try lowering the "ppm" parameter.

38385 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20767 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 Warning: There were 723 peak data insertion problems. Please try lowering the "ppm" parameter.

39145 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 21027 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 38906 m/z ROI's.

Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 20844 Peaks.

Detecting mass traces at 4.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 38504 m/z ROI's.

Detecting chromatographic peaks ... % finish

sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] BiocParallel_1.8.2 CAMERA_1.30.0 xcms_1.50.1 Biobase_2.34.0 ProtGenerics_1.6.0 BiocGenerics_0.20.0 mzR_2.8.1
[8] Rcpp_0.12.16

loaded via a namespace (and not attached): [1] pillar_1.2.1 RColorBrewer_1.1-2 plyr_1.8.4 base64enc_0.1-3 tools_3.3.3 digest_0.6.14
[7] rpart_4.1-13 checkmate_1.8.5 htmlTable_1.11.2 tibble_1.4.2 gtable_0.2.0 lattice_0.20-35
[13] pkgconfig_2.0.1 rlang_0.2.0 igraph_1.2.1 Matrix_1.2-13 graph_1.52.0 rstudioapi_0.7
[19] gridExtra_2.3 stringr_1.3.0 knitr_1.20 cluster_2.0.7 htmlwidgets_1.0 S4Vectors_0.12.2
[25] stats4_3.3.3 multtest_2.30.0 grid_3.3.3 nnet_7.3-12 data.table_1.10.4-3 snow_0.4-2
[31] RBGL_1.50.0 survival_2.41-3 RANN_2.5.1 foreign_0.8-69 latticeExtra_0.6-28 Formula_1.2-2
[37] magrittr_1.5 ggplot2_2.2.1 htmltools_0.3.6 backports_1.1.2 Hmisc_4.1-1 scales_0.5.0
[43] codetools_0.2-15 MASS_7.3-49 splines_3.3.3 MassSpecWavelet_1.40.0 colorspace_1.3-2 stringi_1.1.7
[49] acepack_1.4.1 lazyeval_0.2.1 munsell_0.4.3 `

Thank you.

rietho commented 6 years ago

Hi @Titan100,

thanks for using IPO.

At the moment IPO is in an unsupported state, so I can give only very limited help. It is not clear yet, when and by whom IPO will continue to be supported.

Regarding your issue maybe looking at issue #39 will help you.

Thanks, Thomas

Titan100 commented 6 years ago

Thank you @rietho . Hopefully you will find someone. This tool would be very helpful to add to the metabolomics work flow and keep updating.