Hey there,
I had already a couple of weeks ago some issues with getEIC() (see http://http://www.metabolomics-forum.com/viewtopic.php?f=8&t=384) but since my new problem has nothing to do with that I opened a new topic.
I have an xcmsSet (centWave peak-picked, orbiwarp RT-corrected, grouped, and peaks filled) where two peak groups have a very low m/z difference around 0.0441 and same peak shapes but different abundances and apeces:
> groups( xset )[98:99, ]
mzmed mzmin mzmax rtmed rtmin rtmax npeaks B_Cal D_Cal
[1,] 115.0867 115.0867 115.0868 64.23 63.65 64.75 6 3 3
[2,] 115.1308 115.1293 115.1309 64.62 64.61 64.81 6 3 3
> pks <- peaks( xset )[ unlist( xset@groupidx[ 98:99 ] ), c(1:6,9) ]
> pks
mz mzmin mzmax rt rtmin rtmax maxo
[1,] 115.0868 115.0864 115.0870 63.66 52.62 75.72 631219.562
[2,] 115.0867 115.0861 115.0870 64.75 52.65 75.22 505789.812
[3,] 115.0867 115.0864 115.0868 64.62 52.62 75.66 433946.500
[4,] 115.0868 115.0864 115.0869 63.65 48.54 78.77 513818.281
[5,] 115.0868 115.0864 115.0869 63.84 53.44 75.68 453958.312
[6,] 115.0867 115.0866 115.0868 64.62 52.56 75.66 397969.844
[7,] 115.1308 115.1306 115.1310 64.62 59.64 68.64 19231.410
[8,] 115.1309 115.1303 115.1311 64.75 54.72 71.49 14101.018
[9,] 115.1293 115.1292 115.1294 64.62 59.64 69.66 9610.525
[10,] 115.1309 115.1308 115.1310 64.61 60.59 68.64 15007.605
[11,] 115.1308 115.1307 115.1309 64.81 59.08 69.64 12008.001
[12,] 115.1308 115.1306 115.1309 64.62 59.64 69.66 10699.456
However, getEIC seams obviously to not resolve those peaks:
plot( getEIC( xset, group = 98 ) )
plot( getEIC( xset, group = 99 ) )
[attachment=1:24zorgyy]eics.png[/attachment:24zorgyy]
Even if I specify the mzrange explicitly the mass traces are not resolved:
plot( getEIC( xset, mzrange= pks[ 1:6, 2:3 ] , rtrange = pks[ 1:6, 5:6 ] ) )
plot( getEIC( xset, mzrange= pks[ 7:12, 2:3 ] , rtrange = pks[ 1:6, 5:6 ] ) )
[attachment=0:24zorgyy]eic2.png[/attachment:24zorgyy]
Is it something I am doing wrong or is getEIC just supposed to work like this?
Many thanks in advance,
Isam
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