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 3.0.3
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: 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 3.2.2
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: 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!!!!