Use xcms but mzR occurs error
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1227450726 • 0
@1227450726-24057
Last seen 13 months ago
require(xcms)
require(x13cms)

# set working directory
getwd()
setwd('E:/Example/')
# Peak-picking and retention-time alignment with XCMS
xs= xcmsSet(c('./C12', './C13'),
method= 'centWave',
ppm= 20,
peakwidth= c(20, 200))

Error in xcmsSet(c("./C12", "./C13"), method = "centWave", ppm = 20, peakwidth = c(20,  :
Chromatographic peak detection failed for all files! The first error was: Error in mzR::openMSfile(x, backend = backend): Unable to create valid cRamp object.

1: In serialize(data, node$con) : 载入时'package:stats'可能无用  software error xcms • 246 views ADD COMMENT 0 Entering edit mode '''require(xcms) require(x13cms) getwd() setwd('E:/Example/') xs= xcmsSet(c('./C12', './C13'), method= 'centWave', ppm= 20, peakwidth= c(20, 200))''' Error in xcmsSet(c("./C12", "./C13"), method = "centWave", ppm = 20, peakwidth = c(20, : Chromatographic peak detection failed for all files! The first error was: Error in mzR::openMSfile(x, backend = backend): Unable to create valid cRamp object. 此外: Warning messages: 1: In serialize(data, node$con) : 载入时'package:stats'可能无用

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xcms uses mzR to read data from MassSpec data files. The error message indicates that mzR is not able to read one or more of the files in the folders you specified. This could be either because there are also other files (not only mass spec files) in these directories or that these have a wrong format or a format which mzR does not support.

In addition, I would strongly suggest to change from the old user interface functions (xcmsSet and alike) to the new functions that make use of the MSnbase package to represent the mass spec data. With that it would also much easier to tackle such problems because you first read the data files and can specify which files you actually want to read.

cheers, jo