Chromatographic peak detection failed for all files

[ghost]

I seem to be having problems with your package. I have looked at the previous issues and no one seems to be running into the same problems as I am. I have tried changing the parameters, using both "centwave" and "matchedFilter" but still keep getting errors and the plots produced are blank (empty).

library(IPO) filepath <- "E:/Data/Kundai/RStudio/XCMS/MZXML/KPCI2" files <- list.files(filepath, pattern = "mzXML", recursive = TRUE, full.names = TRUE) peakpickingParameters <- getDefaultXcmsSetStartingParams('centWave') peakpickingParameters$step <- c(0.2, 0.3) peakpickingParameters$fwhm <- c(40, 50)

setting only one value for steps therefore this parameter is not optimized

peakpickingParameters$steps <- 2

time.xcmsSet <- system.time({ # measuring time resultPeakpicking <- optimizeXcmsSet(files = files, params = peakpickingParameters, nSlaves = 1, subdir = NULL, plot = TRUE)

starting new DoE with: fwhm: c(40, 50) snthresh: c(3, 17) step: c(0.2, 0.3) steps: 2 sigma: 0 max: 5 mzdiff: 0 index: FALSE

1 Error in xcms::xcmsSet(files = files, method = "matchedFilter", fwhm = xcmsSetParameters$fwhm[task], : Chromatographic peak detection failed for all files! The first error was: Error in match.arg(params$method, getOption("BioC")$xcms$findPeaks.methods): 'arg' sollte eines von '' sein

Error in resultIncreased(history) : No isotopes have been detected, peak picking not optimizable by IPO! Timing stopped at: 0.31 0.11 71.02

sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

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

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

other attached packages: [1] IPO_1.4.1 CAMERA_1.34.0 rsm_2.9
[4] BiocInstaller_1.28.0 ropls_1.10.0 xcms_3.0.0
[7] MSnbase_2.4.0 ProtGenerics_1.10.0 BiocParallel_1.12.0
[10] mzR_2.12.0 Rcpp_0.12.13 yamss_1.4.0
[13] SummarizedExperiment_1.8.0 DelayedArray_0.4.1 matrixStats_0.52.2
[16] Biobase_2.38.0 GenomicRanges_1.30.0 GenomeInfoDb_1.14.0
[19] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0

[rietho]

Hi!

First, thanks for using IPO :)

I can't see exactly how you got to this error. What's a problem is, that you chose your parameters from the method centWave, while you added parameters for the matchedFilter-method (like fwhm, snthresh, step or steps). This confuses IPO and let's IPO think that you want to use the matchedFilter-method. What confuses me, is that IPO should catch the error in your case. The following part of your code results in a different error:

peakpickingParameters <- getDefaultXcmsSetStartingParams('centWave')
peakpickingParameters$step <- c(0.2, 0.3)
peakpickingParameters$fwhm <- c(40, 50)
#setting only one value for steps therefore this parameter is not optimized
peakpickingParameters$steps <- 2

resultPeakpicking <- optimizeXcmsSet(files = files,
                                     params = peakpickingParameters,
                                     nSlaves = 1,
                                     subdir = NULL,
                                     plot = TRUE)
#+ Error in checkParams(params, quantitative_parameters, qualitative_parameters,  : 
#+   The parameter(s) sigma, max, index is/are missing! Please specify; stopping!

If you want to use the centWave-method, please only specify according parameters. Please see the help of getDefaultXcmsSetStartingParams for more details.

[ghost]

Thank you for your timely response. I have realized that I had mixed up "centwave" and "matchedFilter" options. This is because, after looking up at the previous issues to ensure that I was not repeating an already solved issue, I ended up mixing the code in the vignette and the one used by S Neumann in the last recently solved issue. The software works as shown in the vignette, thank you for your help and for making the package available.

[rietho]

You're welcome.