I changed my computer and re-installed the whole packages, with the latest R version (3.5.1). Since then, xcms does not work anymore, remaining stacked at the first line
Hi everybody, I\'m performing large-scale LCMS metabolomic profiling, and I\'m looking for a R script that performs quality control-based robust LOESS signal correction to correct for analytical drift within and across analytical batches (such as in Dunn, W. B., Broadhurst, D., Begley, P., Zelena, E., Francis-McIntyre, S., Anderson, N., Brown, M., Knowles, J. D., Halsall, A. et al. (2011) Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc 6: 1060-1083). I would be extremely pleased if somebody could help, thanks and see you in washington
Hi there, I'm facing an unresolved problem; we are using a qexactive + in dual mode (+/-) @30000 mass resolution. After conversion into mzXML, we discovered that some features intensity are eratically reported in the diffreport table .tsv, whereas both the EIC caption and also the raw EIC are excellent. See figures below as an illustration I would really appreciate help since we tested many different scripts without any subtantial improvements thank you
raw xcalibur EIC [attachment=2:8i42r00r]xcalibur raw EIC.JPG[/attachment:8i42r00r]
I'm using a q-exactive plus connected to a uplc through an ESI source. After using xcms, the differport matrix contains a lot (too much) of variables with zero intensities, mainly in the samples, less so in the QC's. Here is the script I use
Hi, I would like to process my data but not using fillpeaks. Hereafter is the return I got:
> reporttab<-diffreport(xset2,"échantillons","pools","urines_par_ech",10,metlin=0.15,h=480,w=640) Erreur dans .local(object, ...) : NA values in xcmsSet. Use fillPeaks() any idea how to circumvent this problem and to get to the reporttab step?
