different versions R influence the result of XCMS grouping?? November 10, 2015, 10:38:35 AM Hi everyone,I meet a very very strange situation!I use XCMS for peak detection in R version 3.2.2. Then I try to use the IPO package to optimize the grouping parameters. However, IPO is not available for R 3.2.2. In this case, I change my R to 3.0.3 version. Here, I get the optimized parameters of bw and mzwid after IPO.By using exactly same xcms object, as shown below:> hilicNEG_XS_re An "xcmsSet" object with 152 samples Time range: 3-749.6 seconds (0.1-12.5 minutes) Mass range: 34.9684-1599.6728 m/z Peaks: 1064740 (about 7005 per sample) Peak Groups: 0 Sample classes: Batch_A.QA, Batch_B.QB, Batch_C.QC, Batch_D.QD, Batch_E.QE, Batch_F.QF, Batch_G.QG, Batch_H.QH, Batch_A.Ref, Batch_B.Ref, Batch_C.Ref, Batch_D.Ref, Batch_E.Ref, Batch_F.Ref, Batch_G.Ref, Batch_H.Ref, Batch_A.SA, Batch_B.SB, Batch_C.SC, Batch_D.SD, Batch_E.SE, Batch_F.SF, Batch_G.SG, Batch_H.SH Profile settings: method = bin step = 0.1 Memory usage: 92.2 MB If I DO GROUPING IN R VERSION 3.0.3, I have only 4850 groups, but I get Peak Groups: 16490 when I use VERSION 3.2.2!!!!!!!!!!! :shock: :shock: :shock: :shock: :shock: :shock: 1. VERSION 3.0.3An "xcmsSet" object with 152 samples Time range: 3-749.6 seconds (0.1-12.5 minutes) Mass range: 34.9684-1599.6728 m/z Peaks: 1064740 (about 7005 per sample) Peak Groups: 4850 Sample classes: Batch_A.QA, Batch_B.QB, Batch_C.QC, Batch_D.QD, Batch_E.QE, Batch_F.QF, Batch_G.QG, Batch_H.QH, Batch_A.Ref, Batch_B.Ref, Batch_C.Ref, Batch_D.Ref, Batch_E.Ref, Batch_F.Ref, Batch_G.Ref, Batch_H.Ref, Batch_A.SA, Batch_B.SB, Batch_C.SC, Batch_D.SD, Batch_E.SE, Batch_F.SF, Batch_G.SG, Batch_H.SH Profile settings: method = bin step = 0.1 Memory usage: 100 MB 2. R VERSION 3.2.2An "xcmsSet" object with 152 samples Time range: 3-749.6 seconds (0.1-12.5 minutes) Mass range: 34.9684-1599.6728 m/z Peaks: 1064740 (about 7005 per sample) Peak Groups: 16490 Sample classes: Batch_A.QA, Batch_B.QB, Batch_C.QC, Batch_D.QD, Batch_E.QE, Batch_F.QF, Batch_G.QG, Batch_H.QH, Batch_A.Ref, Batch_B.Ref, Batch_C.Ref, Batch_D.Ref, Batch_E.Ref, Batch_F.Ref, Batch_G.Ref, Batch_H.Ref, Batch_A.SA, Batch_B.SB, Batch_C.SC, Batch_D.SD, Batch_E.SE, Batch_F.SF, Batch_G.SG, Batch_H.SH Profile settings: method = bin step = 0.1 Memory usage: 100 MB What is going on here?? Looking forward your reply!!!! Quote Selected