Metabolomics Society Forum

Hi,

the file you sent loads fine over here, so I expect something in your installation.
If the smaller files load fine, I suspect RAM issues. How much memory do you have ?

Code: [Select]

> library(xcms)
Loading required package: mzR
Loading required package: Rcpp
xr <- xcmsRawLoading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
    lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

("data2
Attaching package: ‘xcms’

The following object is masked from ‘package:Biobase’:

    phenoData, phenoData<-

> xr <- xcmsRaw("data2.cdf")
> xr
An "xcmsRaw" object with 13257 mass spectra

Time range: 360-4204.2 seconds (6-70.1 minutes)
Mass range: 14.9984-519.9868 m/z
Intensity range: 0-1384450 

MSn data on  0  mass(es)
	with  0  MSn spectra
Profile method: bin 
Profile step: 1 m/z (506 grid points from 15 to 520 m/z)

Memory usage: 5110 MB
> sessionInfo()
R version 3.0.0 Patched (2013-04-04 r62494)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] xcms_1.43.1        Biobase_2.22.0     BiocGenerics_0.8.0 mzR_2.1.10        
[5] Rcpp_0.11.2       

loaded via a namespace (and not attached):
[1] codetools_0.2-14 zlibbioc_1.8.0  

The matrix that you get has the dimensions:

Code: [Select]

> dim(xr@env$profile)
[1]   506 13257

So the 13257 correspond to the scans, the 506 grid points from 15 to 520 m/z.

Yours,
Steffen

Hi,
if your installation works in principle, there is little I can think of.
Is this LECO GCxGC data ?

If your file has  6,479,713  bytes, that's only 6MB, so not huge at all.

For your other question, if you get the xcmsRaw, you find the
Raw data as a matrix by using xr@env$profile if you've set profStep=1
where 1 is the resolution in Da of the matrix.

Yours,
Steffen