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Messages - edammer

XCMS / Re: xcmsSet centWave

November 14, 2014, 06:03:32 PM

Hi all,

I get past the error by removing mslevel=1 from the parameters.

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

XCMS / 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