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1
XCMS / Re: How to access data returned by getEIC?
I have answered my own question after a good night's sleep.
Code: [Select]
temp <- attr(eicm,"eic")
rtime <- temp$xcmsRaw[[1]][,1] # get rt's
intensity <- temp$xcmsRaw[[1]][,2] # get intensities
Sorry for the noise.
2
XCMS / How to access data returned by getEIC?
I am a dill and a dodo with failing Google fu,

I can open a data file in R with
Code: [Select]
filename <- "#4606.mzXML"
xraw <- xcmsRaw(filename)
and get an extracted ion chromatogram with
Code: [Select]
mzr <- cbind(179.9,180.3)
rtr <- cbind(397,1560.3)
eicm <- getEIC(xraw, mzrange = mzr, rtrange = rtr)
but for further processing I would now like to access the values for 'rt' and 'intensity' as displayed by
Code: [Select]
> attr(eicm,"eic")
$xcmsRaw
$xcmsRaw[[1]]
              rt  intensity
   [1,]  397.022       1425
   [2,]  397.241      13700
...
[5510,] 1560.069          0
[5511,] 1560.288      36000
Could somebody please help with the required voodoo?

TIA
5
XCMS / Re: xcms & mzR installation problem
This is probably not the same problem, but I very recently updated to R-2.15.0 and then tried to install xcms. My initial attempt failed due to the version of mzR that was downloaded using the installation procedure at http://metlin.scripps.edu/xcms/installation.php failing to compile on my Linux 64-bit system with gcc-4.7. I manually downloaded the mzR_1.3.7.tar.gz source package from http://www.bioconductor.org/packages/2. ... 3.7.tar.gz and built the package from within R using install.package(c("/<path>/<to>/mzR_1.3.7.tar.gz")). With that in place, xcms was able to be successfully installed.