Hello!
I was wondering if fillPeaks always calculates the right intensities. Here an example:
[attachment=0:1pmk1zva]findPeaks.png[/attachment:1pmk1zva]
[attachment=1:1pmk1zva]fillPeaks.png[/attachment:1pmk1zva]
The peak is correctly identified by fillPeaks but the intensity is to high compared to the peak from findPeaks.
sessionInfo:
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=de_AT.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_AT.UTF-8 LC_COLLATE=de_AT.UTF-8
[5] LC_MONETARY=de_AT.UTF-8 LC_MESSAGES=de_AT.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_AT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
best regards
Gunnar
[attachment deleted by admin]
Are you sure this intensity is a result of fillPeaks(), and not caused by a retention time correction/alignment problem ?
A peak with an intensity of 2e6 should have been detected at the first place !
Hello Ralf,
we had a closer look into the raw data and may have found the origin of the problem:
Measurements were made with a LC/FTICR-MS system (LC coupled to Thermo LTQ FT Ultra) which produces data with quiet a high resolution. In the raw-files with the high intensities is a very small peak, therefore not found by findPeaks. Unfortunately nearby (~60ppm and same RT) is a high peak which is later filled in by fillPeaks. That led to the clue that the step-width of fillPeaks was to wide. Since step is taken from the xcms-object we added
profparam = list("step" = 0.01)
to the xcmsSet-parameters.
Now fillPeaks looks in a more narrow mz-slice and, as far as we can say, chooses the right peak.
best regard
PS:
that also benefits EIC-diagrams which are more accurate now :-)