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Topics - osuct

1
XCMS / help interpreting result
So my data is generated using Waters UPLC/QTOF-MS

I ran the following command in xcms:
Code: [Select]
xset <- xcmsSet(method="centWave")
xset <- group(xset)
xset@groups
         mzmed     mzmin     mzmax    rtmed   rtmin   rtmax npeaks samples
 [1,]  90.52499  90.50587  90.53768 566.7325 493.651 571.501    602     434
 [2,]  96.96339  96.96293  96.96393 573.6620 572.318 574.551    432     432
 [3,]  97.99267  97.96968  97.99426 570.5130 568.622 573.041    819     432
 [4,]  98.51168  98.51125  98.52936 569.8830 480.473 571.088    441     440
 [5,] 102.03374 102.03304 102.12967 567.2895 467.341 570.347    544     503
 [6,] 111.98470 111.98376 112.03649 571.1140 535.050 572.944    545     462
 [7,] 113.96607 113.96540 113.97762 571.2150 493.610 575.702    434     433
 [8,] 118.12385 117.93697 118.12470 551.8370 433.981 580.286   1192     432
 [9,] 125.98792 125.97683 125.98878 567.3455 490.244 570.640    436     432
[10,] 128.95311 128.95244 128.95365 571.7455 571.056 572.930    432     432
[11,] 141.96116 141.96064 141.98669 571.6450 478.937 572.517    448     432
[12,] 145.93201 145.93138 145.93242 574.9675 573.559 576.317    432     432
[13,] 149.02481 149.02377 149.04653 490.3790 415.157 546.035    568     558
[14,] 158.96294 158.96252 158.96682 572.2490 517.538 573.042    434     432
[15,] 171.15070 171.10154 171.17518 163.7375 105.204 261.115    722     717
[16,] 186.95823 186.95770 186.95874 571.7560 570.904 572.583    432     432
[17,] 187.12794 186.95827 187.15414 206.0160 205.260 263.677    521     516
[18,] 550.63239 550.55762 550.63547 505.1365 498.520 555.740    462     432
[19,] 551.63567 551.55751 551.63963 504.9905 498.503 520.841    442     432

It looks like the program identified 19 peak groups. That means there are 19 analytes identified across multiple samples?
The first analyte is eluting at 566.7325 retention time (median) which has 602 peaks and it appears in 434 samples?

From another thread, I read that I don't have to do retention time correction for UPLC/QTOF. Can anyone tell me why?

Thanks in advance!
2
XCMS / unable to create xcms object
Dear All,

I have been trying to create xcms object using the command
Code: [Select]
xset <- xcmsSet()
after changing the directory to where my CDF files is. I got the following error:
"Error in logical(nrow(m)): invalid 'length' argument"
This is if I tried to process the positive data. When I tried to process the negative spectra, I got the following error:
"error in rmat[,"rt"]:incorrect number of dimensions. Any idea what happen? Thanks in advance for your help.

The following is the traceback associated with the error in rmat.
Code: [Select]
> traceback()
8: .local(object, ...)
7: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
6: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
5: do.call(method, list(object, ...))
4: .local(object, ...)
3: findPeaks(lcraw, ...)
2: findPeaks(lcraw, ...)
1:
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] multtest_2.12.0 Biobase_2.14.0  xcms_1.32.0     mzR_1.2.2      
[5] Rcpp_0.9.13    

loaded via a namespace (and not attached):
[1] codetools_0.2-8  MASS_7.3-19      splines_2.15.1   stats4_2.15.1   
[5] survival_2.36-14 tools_2.15.1