I am looking at the XCMSOnline log, and I see that the FillPeaks row is left blank. I would have expected it to default to chrom. Is this the case, or do I assume FillPeaks was not applied?
Does metaXCMS use the XCMS Online statistics results? Are they normalized? I ran the pairwise analysis using a Welch's t-test but now I am wondering if this was the wrong approach because the data do not have a normal distribution (this became apparent when I used MetaboAnalyst). I thought the data were normalized to TIC, but based on my reading it seems that I am mistaken.
