Re: Calculate Intensity/Abundance
Reply #3 –
plasma33,
So when you get your diffreport you should see that you get something like the following columns:
"mzmed" "mzmin" "mzmax" "rtmed" "rtmin" "rtmax" "npeaks" "KO" "WT" "ko15" "ko16" "ko18" "ko19" "ko21" "ko22" "wt15" "wt16" "wt18" "wt19" "wt21" "wt22"
The example above is for the faahKO toy data set. Each file has the intensity values for each feature. So for file ko15 the intensity for 200.1m/z @ 2926s the intensity is 147887.
mzmed mzmin mzmax rtmed rtmin rtmax npeaks KO WT ko15 ko16
200.100 200.100 200.100 2926.264 2876.967 2931.740 10.000 5.000 5.000 147887.526 451600.713
ko18 ko19 ko21 ko22 wt15 wt16 wt18 wt19 wt21 wt22
65290.385 NA 91635.445 162012.439 175177.079 82619.480 NA 69198.222 153273.469 98144.280
As far as metlin searching goes you should only need the m/z and retention times for the search. If however, you are looking for MS/MS searching (where you'll need the intensity values for searching) you'll need to read and following:
http://www.bioconductor.org/packages/re ... cmsMSn.pdf
hope it's helpful.
Paul