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Messages - flolai

1
XCMS / Re: Consequences of using Centwave for profile mode data
Dear Jan,

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



2
XCMS / Consequences of using Centwave for profile mode data
Dear All,

I am trying to reproduce/reprocess a recently published data (data was open to public) and I found out that the author used centwave algorithm to process profile mode data (version of R used 3.2, she used a wrap around function for xcms peak picking so I can't tell which version of xcms she used). I would like to know if there will be any negative effect on the final data table using her method. As far as I know, xcms online will not accept using centwave for profile mode data?

Many thanks for your help

Flo