msNormalizeTIC: Intensity Normalization Using Total Ion Current

In zeehio/msProcess: Protein Mass Spectra Processing

Description

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.

Usage

msNormalizeTIC(x, process="msNormalizeTIC")

Arguments

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".

Value

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".

References

E.T. Fung and C. Enderwick, ProteinChip clinical proteomics: computational challenges and solutions, Biotechniques, Supplement 32:S34-S41, 2002.

See Also

msNormalize, msNormalizeSNV.

Examples

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)

zeehio/msProcess documentation built on May 4, 2019, 10:15 p.m.