Error in profEIC

[yhshengjy]

Hi, when i use xcmsSet "getEIC" method, I am getting this issue: xset = xcmsSet(fn, method = "centWave", peakwidth = c(5,20), ppm = 10, snthresh = 6, mzdiff = 0.01, prefilter = c(3,100), noise=100) getEIC(xset,mzrange=matrix(xset@peaks[1970,c("mzmin","mzmax")],nrow = 1))

Error in profEIC(object, mzrange = mzrange, rtrange = rtrange, step = step) : 'mzrange' number 1 (49.4987898377907, 49.4993976984236) is outside of the mz value range of 'object'

file:StdMixLow.zip

sessionInfo()

R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] xcms_3.8.2 MSnbase_2.12.0 ProtGenerics_1.18.0 S4Vectors_0.24.4 mzR_2.20.0 Rcpp_1.0.5
[7] BiocParallel_1.20.1 Biobase_2.46.0 BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] vsn_3.54.0 tidyr_1.1.3 splines_3.6.0 foreach_1.5.0 assertthat_0.2.1
[6] statmod_1.4.34 BiocManager_1.30.10 affy_1.64.0 robustbase_0.93-6 impute_1.60.0
[11] numDeriv_2016.8-1.1 pillar_1.6.1 backports_1.1.7 lattice_0.20-38 glue_1.4.1
[16] limma_3.42.2 digest_0.6.25 RColorBrewer_1.1-2 minqa_1.2.4 colorspace_1.4-1
[21] preprocessCore_1.48.0 Matrix_1.2-17 plyr_1.8.6 MALDIquant_1.19.3 XML_3.99-0.3
[26] pkgconfig_2.0.3 broom_0.7.6 zlibbioc_1.32.0 purrr_0.3.4 scales_1.1.1
[31] RANN_2.6.1 affyio_1.56.0 lme4_1.1-23 tibble_3.1.1 generics_0.0.2
[36] IRanges_2.20.2 ggplot2_3.3.3 ellipsis_0.3.2 MassSpecWavelet_1.52.0 survival_3.2-7
[41] magrittr_2.0.1 crayon_1.4.1 ncdf4_1.17 fansi_0.4.1 doParallel_1.0.15
[46] nlme_3.1-139 MASS_7.3-51.4 tools_3.6.0 lifecycle_1.0.0 munsell_0.5.0
[51] pcaMethods_1.78.0 compiler_3.6.0 mzID_1.24.0 rlang_0.4.11 grid_3.6.0
[56] nloptr_1.2.2.2 iterators_1.0.12 boot_1.3-22 gtable_0.3.0 codetools_0.2-16
[61] lmerTest_3.1-2 multtest_2.42.0 DBI_1.1.0 R6_2.4.1 dplyr_1.0.6
[66] utf8_1.1.4 vctrs_0.3.8 DEoptimR_1.0-8 tidyselect_1.1.0 `

thanks

[jorainer]

May I suggest to use the new functions instead of the deprecated xcmsSet code? That will also make it easier for me to find the origin of the problem. Also, if I remember correctly, getEIC was calculating first the profile matrix binning data along the m/z dimension. Thus the returned EIC was not exactly representing the raw data (on which centWave performed the peak detection).

You should be able to do the same as above with:

data <- readMSData(fn, mode = "onDisk")
cwp <- CentWaveParam(
    peakwidth = c(5, 20),
    ppm = 10,
    snthresh = 6,
    mzdiff = 0.01, 
    prefilter = c(3, 100),
    noise = 100)
xdata <- findChromPeaks(data, cwp)

eics <- chromatogram(xdata, mz = chromPeaks(xdata)[1970, c("mzmin", "mzmax")])