Dear all:
I believe that many people encounter such kind of question, XCMS and Progenesis QI, two kind of softwares who is better or more accuracy? Now I have a project, it contains many cell samples, the samples were analyzed in waters synapt G2 Si and the raw data was converted into the netCDF format by databridge software. Then the CDF files were processing by XCMS and QI, Finally, the table list had a large difference. the table list of XCMS is about 17000 features and the QI only is about 7000 features. So I am not sure who is better ? Maybe many nosie features go into the XCMS table list or maybe the QI lost the important features? Base on the example, I hope we may discuss the data processing workflow , how to ensure that the real difference existing in the raw data could be dig accurately by our data processing step ? If necessary, I can upload my R scripts command for everybody check. Thank you
Bset regards!
Bingpeng Yan