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XCMS / Re: Consequences of using Centwave for profile mode data
Many thanks for your reply. That was what I guessed before...so, I emailed the author specifically asking her about her profile data and if she would at least give me her peak picking settings.
According to her, she used 2ppm (I honestly surprised) , mzdiff = 0.001 and she did not centroid her data.....and reported 800 analytes in her paper.
I tried to repeat her settings in xcms, it has taken 2 days now and it's still running (when I used some sensible settings, 10 ppm and convert to centroid data, it only took a few hours).
What I am really worried about is the final data quality as I need to integrate these results with transcriptomics data. I would like to be accurate if I need to criticise her result in my MSc project.
Many thanks.
Flo