Error in Fillpeaks

Workflow4Metabolomics LCMS
#1

I met a problem with fillpeaks, whit the following error :

Defining peak areas for filling-in .... OK
Start integrating peak areas from original files
Requesting 751 peaks from T05_05C1.mzXML ... Error in binYonX(mz, int, breaks = brks, fromIdx = fromIdx, toIdx = toIdx,  : 
  'fromIdx' has to be smaller than 'toIdx'!
Calls: fillChromPeaks ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

Can someone help me to identify what represent fromIdx and toIdx, please?

Thanks
Cédric

#2

I searched a little about this error before contacting the xcms developers.


In this thread, it is said:

The problem occurred if the data was subset to an m/z range for which no signal was present in some spectra (or in general if the data contained empty spectra).

If it doesn't make sense to you or @team.w4m, I will write an issue in https://github.com/sneumann/xcms/issues

#3

I read the thread about binYonX you tagged. It seems consistant with the fact that fillPeaks in particular is searching for content in areas that have been previously considered as not containing 'sufficiently good' peaks (excuse the werd expression), which includes potentially 'empty' zones.

I vote for the issue reporting.

#4

Hop: https://github.com/sneumann/xcms/issues/519
:crossed_fingers:

#5

I just see @gildaslecorguille that the developper ask for examples/data :slight_smile:

Don't hesitate @ced.leroux to provide some examples directly on the issue if you can: Fillpeaks - Error in binYonX · Issue #519 · sneumann/xcms · GitHub