I am using netCDF files data. (Waters), so to correct the Lock Mass Gap, I did selected the option "Correct mass calibration gaps" on the micellaneous of my method parameters, Online XCMS. I got this warning after processing my data :
Warning : Correction of mass calibration gaps failed (AutoLockMass). Processing data without correction.
I do agree with you that the statistics will be very very different.
What I was just asking about is whether the tow matrix generated with both processing #1 is A vs B and #2 is (A u B) vs Blank would be different in terms of number of features, retention time correction ...etc ?
Actually, I was given such data to analyse. I am not intending to perform comparaison on XCMS Online and to use its stat results of course. It's irrelevant since we get different results. I am just wondering if it's relevant to use the matrix generated by (A u B) vs Blank and do statistics by comparing the data A vs B by importing it on other data analysis softwares which with paying attention to exclud Blank data of course ?
Another question :
Since it seems to be a trick for a multi classe comparison not implemented on the actual XCMS release.
e.g : A, B, C, D, E, F : classes
So, could we process (A+B+C) vs (D+E+F), then use the generated matrix for data analysis on other softwares (multivariate, pairewise analysis etc ...) e. g : A vs B , A vs F , B vs C, ... etc ?
Do we get the same features, so the same diffreport, by processing 2 groups downloaded in 2 different datasets in one case, and by processing the same 2 groups downloaded in one dataset against blank samples in the other dataset ?
The same processing parameters were set in both methods.
