Dear all,

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()
[1] TRUE
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] BiocInstaller_1.16.0

loaded via a namespace (and not attached):
[1] 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?   

Many thanks,

Sydney Liu Lau

University of NSW (Australia)

I don't think you want to use system.file() in this case. 

"test" should be defined as follows:

test<- "C:/Users/User/Documents/MA3_PAD_T_x2.mzXML"

But make sure that it exists:

file.exists(test)

Should return TRUE.

Dan

Hi Dan,

I have made the change and it works now.  Thank you so much for your help and quick response; it is much appreciated.

Kindest regards,

Sydney