I am a very new user of R and I wanted to test if I could use it to analyse mass spectrometry data in mzXML format. I believe I have correctly installed the Bioconductor package, and my mzXML files are fine (I have been able to visualise them using PEAKS).
I am following the instructions in the mzR package - unfortunately I am already stuck at the first hurdle (highlighted in yellow). Here is what I have done so far (I have also included information about my session below):
> library(mzR) Loading required package: Rcpp > library(msdata) > test<-system.file("C:/Users/User/Documents/MA3_PAD_T_x2.mzXML", package="msdata") > aa<-openMSfile(test) Error in openMSfile(test) : File not found.
> library(BiocInstaller) Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help > biocValid()  TRUE > sessionInfo() R version 3.1.1 (2014-07-10) Platform: i386-w64-mingw32/i386 (32-bit) locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.16.0 loaded via a namespace (and not attached):  tools_3.1.1 I converted my Thermo .raw files to mzXML using ProteoWizard and I can visualise them using PEAKS. What am I missing here?
Sydney Liu Lau
University of NSW (Australia)