msNormalizeTIC {msProcess} | R Documentation |
Normalizes a set of spectra using the total ion current (TIC). Each TIC is calculated as the sum of the intensities. The intensity of a spectrum is divided by its TIC and then multiplied by the median TIC of the set of spectra.
msNormalizeTIC(x, process="msNormalizeTIC")
x |
An object of class msSet . |
process |
A character string denoting the name of the
process to register with the (embedded) event history object of the input
after processing the input data. This process is not updated if it
already exists in the event history. Default: "msNormalizeTIC" . |
An object of class msSet
such that the normalized spectra
have the same AUC (the median of the AUCs of spectra).
The TIC's are attached as element "tic"
.
E.T. Fung and C. Enderwick, ProteinChip clinical proteomics: computational challenges and solutions, Biotechniques, Supplement 32:S34-S41, 2002.
msNormalize
, msNormalizeSNV
, colSums
.
if (!exists("qcset")) data("qcset", package="msProcess") ## extract several spectra from the build-in ## dataset z <- qcset[, 1:8] ## denoising z <- msDenoise(z, FUN="wavelet", n.level=10, thresh.scale=2) ## baseline subtraction z <- msDetrend(z, FUN="monotone", attach=TRUE) ## intensity normalization z <- msNormalizeTIC(z) ## visualize the normalization plot(z, process="msNormalize", subset=1:8, xlim=c(13000, 17000), lty=c(1,4), lwd=1:2)