[R] Attempting to confirm a program i wrote in C (normalize 2 datasets, transform into histogram, transform into CDF, perform KS test)

Tarskin b.c.jansen at lumc.nl
Mon Jan 28 09:39:47 CET 2013

The C program takes 2 mzML files from which the binary strings (according to
the X data and Y data is uncompressed/decoded), it then examines spectral
(xy data) similiary and combines both datasets into a new one and finally
after all similar spectra have been merged it writes it all back into 1 new
mzML file. I am assuming that people do not want to get several complete
mzML files however, I will however include 2 spectra from different sources
that were extracted from the total mzML files that I have been using to test
this with.

IgG2_G1F.data <http://r.789695.n4.nabble.com/file/n4656833/IgG2_G1F.data>  
IgG2_G1F.data <http://r.789695.n4.nabble.com/file/n4656833/IgG2_G1F.data>  

The steps i performed in R:

experimental<-read.table(<first data set>, header=T)
predicted<-read.table(<second data set>,header=T)
hist_e<-hist(rep(experimental[,1],experimental[,2]), breaks=seq(0,2500,1))
-- up to here it does what I expect, my own C program would now transform
the GSL hist object to a GSL cdf object --
ecdf(hist_p) seemed the logical choice to me however it complains about
error in rank and my attempts to figure out what this means haven't been
very clear so far.

I would appreciate any pointer saying why this doesn't do what I'm

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