Sure it does look like it is the same object though (I am trying to do things really as simple as possible so I am just using the nice simple generic object "A" for all my xcms work) This is in the command line, so I'll put in my commands into the code block with the ">" to start off something I typed in and follow it with the output (abridged to the first object output in the case of long repetitive outputs such as xcmsSET).
> A<-xcmsSet(method="centWave", mzdiff=-0.5, ppm=4000, scanrange = c(40,800))
Sample1:
Detecting mass traces at 4000 ppm ...
% finished: 10 20 30 40 50 60 70 80 90 100 Warning: There were 116247 peak data insertion problems.
Please try lowering the "ppm" parameter.
4085 m/z ROI's
Detecting chromatographic peaks ...
% finished: 10 20 30 40 50 60 70 80 90 100
322 Peaks.
##ABRIDGED ...
> group(A)
163 226 288 351 413 476 538 601 663 726 788 851 913 976
> retcor(A, family="s", plottype="m", method="linear")
Error in .local(object, ...) : No group information found
> group(A, bw=c(5,20), mzwid=0.5)
225 350 475 600 725 850 975
There were 50 or more warnings (use warnings() to see the first 50)
> retcor(A, family="s", plottype="m", method="linear")
Error in .local(object, ...) : No group information found
> Reporttab<-diffreport(A, "runs", "control", "centWaveTry1", 5)
Error in .local(object, ...) : No group information found
I just tried this all again except with "ppm=400" in the xcmsSet function and got basically all the same results except it found many fewer peaks in each file and didn't warn about setting the ppm low, but I still got the exact same resulting failure from group, retcor, ect...