Very basic Question on mzML

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Very basic Question on mzML

October 18, 2013, 11:50:55 AM

Hi everyone,
a very basic question but I'd be really grateful if you could help me: I'm trying to load a set of mzML files saved in a single folder into XCMS. So far I tried doing this:
mzMLpath <- ("~/path")
mzMLfiles <- list.files(mzMLpath,recursive=TRUE,full.names=TRUE)

LCMS <-xcmsRaw (mzMLfiles)

what am I doing wrong? Do i need to read each mzML file separately?

Re: Very basic Question on mzML

Reply #1 – October 19, 2013, 08:07:34 AM

XR <- xcmsSet(mzXMLfiles) # load files in path into a xcmSet object

Re: Very basic Question on mzML

Reply #2 – October 19, 2013, 03:49:29 PM

Yep!

xcmsRaw - object for single file.
xcmsSet - objects for multiple files ie set of xcmsRaw objects

## not to confuse things but
xcmsEIC - object for holding EIC data for plotting

Have a read through the documentation and tutorial! Very helpful!
http://www.bioconductor.org/packages/re ... rocess.pdf

Re: Very basic Question on mzML

Reply #3 – October 20, 2013, 12:19:57 PM

thanks, it's a lot easier after reading the manual :oops: