xcmsSet centWave November 12, 2014, 07:35:48 PM I am trying to run xcms on 14 mzXML LC-MS/MS proteomic runs for peak detection and alignment and get the following error:xs <- xcmsSet(files=mzdatafiles, method="centWave", mslevel=1, ppm=4, peakwidth=c(2,30), snthresh=10, prefilter=c(7,10000), mzCenterFun="wMean", integrate=1, mzdiff=-0.001, fitgauss=FALSE, noise=10000, sleep=0, verbose.columns=FALSE)Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘findPeaks.centWave’ for signature ‘"missing"’However, when I run peak detection with the same parameters:xraw <- xcmsRaw(mzdatafiles[1], includeMSn=TRUE)peaks <- findPeaks.centWave(xraw, ppm=4, peakwidth=c(2,30), snthresh=10, prefilter=c(7,10000), mzCenterFun="wMean", integrate=1, mzdiff=-0.001, fitgauss=FALSE, scanrange= numeric(), noise=0, sleep=0, verbose.columns=FALSE, ROI.list=list()) Detecting mass traces at 4 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 26511 m/z ROI's. Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 7414 Peaks.I do not get an error. Please let me know how I can get an xcmsSet object with roughly the above parameters and centWave method of peak detection?Best regards and thanks in advance.my sessionInfo:R version 3.1.0 (2014-04-10)Platform: x86_64-w64-mingw32/x64 (64-bit)locale:[1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252[4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages:[1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages:[1] snow_0.3-13 xcms_1.40.0 Biobase_2.24.0 [4] BiocGenerics_0.10.0 mzR_1.10.7 Rcpp_0.11.3 loaded via a namespace (and not attached):[1] codetools_0.2-9 tools_3.1.0 Quote Selected
Re: xcmsSet centWave Reply #1 – November 13, 2014, 02:21:40 AM What exactly is the content of mzdatafiles?What does traceback() say? Quote Selected
Re: xcmsSet centWave Reply #2 – November 13, 2014, 09:09:45 AM Hi Jan and thanks.mzdatafiles are 14 peptide run RAW data files from an Orbi-XL converted by readw to mzXML. Total file size is ~1.7 GB and I have 16GB RAM. Note that findPeaks.centWave() (which works) is only running on the first of the 14 files. xcmsSet() does run, but only with method="MS1", where I am hoping that centWave method and its parameters will do a better job of separating out peptide features for subsequent grouping and retcor().> mzdatapath <- "e:/IMAC_7x7x7mzXML/"> list.files(mzdatapath, recursive = TRUE) [1] "AD/AD_0500_12.mzXML" "AD/AD_0500_52.mzXML" "AD/AD_0503_163.mzXML" [4] "AD/AD_e04_186.mzXML" "AD/AD_e05_04.mzXML" "AD/AD_e06_158.mzXML" [7] "AD/AD_e08_53.mzXML" "CT/ctl_0500_06.mzXML" "CT/ctl_0503_299.mzXML"[10] "CT/ctl_0503_35.mzXML" "CT/ctl_0503_390.mzXML" "CT/ctl_a86_46.mzXML" [13] "CT/ctl_e05_130.mzXML" "CT/ctl_e06_41.mzXML" > mzdatafiles <- list.files(mzdatapath, recursive = TRUE, full.names = TRUE)> xs <- xcmsSet(mzdatafiles, method="centWave", mslevel=1, ppm=4, peakwidth=c(2,30), snthresh=10, prefilter=c(7,10000), mzCenterFun="wMean", integrate=1, mzdiff=-0.001, fitgauss=FALSE, noise=10000, sleep=0, verbose.columns=FALSE)Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘findPeaks.centWave’ for signature ‘"missing"’> traceback()7: stop(gettextf("unable to find an inherited method for function %s for signature %s", sQuote(fdef@generic), sQuote(cnames)), domain = NA)6: (function (classes, fdef, mtable) { methods <- .findInheritedMethods(classes, fdef, mtable) if (length(methods) == 1L) return(methods[[1L]]) else if (length(methods) == 0L) { cnames <- paste0(""", sapply(classes, as.character), """, collapse = ", ") stop(gettextf("unable to find an inherited method for function %s for signature %s", sQuote(fdef@generic), sQuote(cnames)), domain = NA) } else stop("Internal error in finding inherited methods; didn't return a unique method", domain = NA) })(list("missing"), function (object, ...) standardGeneric("findPeaks.centWave"), <environment>)5: findPeaks.centWave(ppm = 4, peakwidth = c(2, 30), snthresh = 10, prefilter = c(7, 10000), mzCenterFun = "wMean", integrate = 1, mzdiff = -0.001, fitgauss = FALSE, noise = 10000, sleep = 0, verbose.columns = FALSE)4: do.call(method, params)3: FUN(X[[1L]], ...)2: lapply(argList, findPeaksPar)1: xcmsSet(mzdatafiles, method = "centWave", mslevel = 1, ppm = 4, peakwidth = c(2, 30), snthresh = 10, prefilter = c(7, 10000), mzCenterFun = "wMean", integrate = 1, mzdiff = -0.001, fitgauss = FALSE, noise = 10000, sleep = 0, verbose.columns = FALSE)The header of a mzXML file:<?xml version="1.0" encoding="ISO-8859-1"?><mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1 http://sashimi.sourceforge.net/schema_r ... dx_3.1.xsd" > <msRun scanCount="11270" startTime="PT0.5806S" endTime="PT4799.83S" > <parentFile fileName="AD_0500_12.RAW" fileType="RAWData" fileSha1="070f5771336b6946c76bb8f845c8ed042023cab2" /> <msInstrument> <msManufacturer category="msManufacturer" value="Thermo Scientific" /> <msModel category="msModel" value="LTQ Orbitrap XL" /> <msIonisation category="msIonisation" value="NSI" /> <msMassAnalyzer category="msMassAnalyzer" value="FTMS" /> <msDetector category="msDetector" value="unknown" /> <software type="acquisition" name="Xcalibur" version="2.5.5" /> </msInstrument> <dataProcessing centroided="1" > <software type="conversion" name="ReAdW" version="4.3.1(build Sep 9 2009 12:30:29)" /> </dataProcessing>-Eric Quote Selected
Re: xcmsSet centWave Reply #3 – November 14, 2014, 06:03:32 PM Hi all, I get past the error by removing mslevel=1 from the parameters. Quote Selected