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Topics - DanielWillems

R / Analyzing data that has been devided from one file into multiple files
I have some data that was acquired on an Agilent 6340 ion trap, so low resolution.  The data was acquired in positive mode and all in one 300 minute (5 hour) run.  I have since used proteowizard to "chop it up" into smaller (195 sec) chunks.  I have found that the original timing was retained and the chunks are indeed 195 seconds in length.  The samples were introduced into the MS through a novel device that has very little if any chromatography and thus is much more like direct injections.  To work out the analysis, I am currently working with a small subset of these runs (5 injections).

I also have a set of this data that I have gone into and replaced the original scan data with the scan numbers from just the 1st run in an attempt to group the data per the retention time data.

OK now to the question.  I am using xcmsSet in R to analyze the data.  I have picked peaks with this code:

"xset <- xcmsSet(samples, snthresh= 1.8, method = c("matchedFilter"), step = 0.2, steps = 1)"

and I think I have good results but am unsure how to visualize this data, any suggestions there?  Then when I group using:

"xset <- group(xset)"

It looks OK but again, I am not sure how to visualize this to check.  Finally when I try to RT correct this data across what are now separate files using:

"xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")"

‚ÄčAll I get is an error that says :

"Error in .local(object, ...) : No group information found"

Indeed the picked xset returns  with Peak Groups: 0

Two questions here, 1. is this likely to be because the original retention time data was saved during the file clipping and conversion step?  2.  Is there away around this so I can look for differences in this data?

Thank you so much for any help you can offer,