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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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Error in .local(object, ...) : xcmsSource: file not found: NA #508

Open wanglai786 opened 3 years ago

wanglai786 commented 3 years ago

When I used xcms to group or fillpeaks my data, some error messages happened.Hope someone can help me,thanks a lot

xs= group(xs, bw=5, mzwid=0.025) Processing 75955 mz slices ... OK xs2= retcor(xs, method= 'obiwarp') center sample: M1901502 Processing: NA Create profile matrix with method 'bin' and step 1 ... OK Error in .local(object, ...) : xcmsSource: file not found: NA xs2= group(xs2, bw=5, mzwid=0.025) Error in h(simpleError(msg, call)) : 在为'group'There was an error evaluating the 'object' argument when the function selected the method: object 'xs2' not found xs3= fillPeaks(xs2) Error in h(simpleError(msg, call)) : 在为'fillPeaks'There was an error evaluating the 'object' argument when the function selected the method': object 'xs2' not found View(xs) Error in if (more || nchar(output) > 80) { : missing value where TRUE/FALSE needed Error: no more error handlers available (recursive errors?); invoking 'abort' restart

jorainer commented 3 years ago

Please don't use the old functions (xcmsSet, group etc) anymore. Try to update the workflow to the new functions and objects shown here.

The first error message xcmsSource: file not found: NA tells you that one of your files was not found. Did you move the original files? But again, with the old user functions debugging is much harder.

jorainer commented 3 years ago

Is this issue now solved? Please close if so @wanglai786