Dilution2005Raw {msDilution} | R Documentation |
A data object of class msSet
consisting of 280 MALDI-TOF mass spectra.
These data come from a dilution experiment aimed at elucidating
which features in MALDI-TOF mass spectrometry data are informative
for quantifying peptide content.
The details of the experiment are described in [2].
The primary dataset consists of 250 spectra collected from 5 different serum sources (5 people from a health study), each subject to 10 different concentrations of a peptide mixture that contained several known peptides. Each of the 50 prepared samples were spotted, randomly, 5 times each on a single plate producing a total of 5x10x5 = 250 spectra.
An additional 30 spectra arise from: 2 replicate spectra from each of the 10 concentrations of the peptide mixture, plus 2 replicates of serum-only spectra from each of the 5 serum samples.
NOTE: An error was made during the process of randomly spotting samples to the plate: one of the replicates from concentration 6 was spotted on top of a serum-only sample. The result is that two spectra from this design are missing: serum 1, concentration 6, replicate 4 (sample 36), and serum 4, concentration 0, replicate 1. This left one empty spot on the plate (sample 280) to which a sample containing only cytochrome c was spotted. The latter was not used in any subsequent analysis in [2], and no adjustment was made for former in the analysis in [2] (sample 36 was used as is).
Dilution2005Raw$coding is a list with 6 elements: "dir.org", "cyt.ind", "pep.ind", "ser.ind", "mix.ind", "err.ind". The "dir.org" is a matrix describing the source of the 280 MALDI spectra contained in this dataset. The others are vectors of indices for various types of samples: "cyt.ind" for cytochrome c, "pep.ind" for peptide mixture, "ser.ind" for serum-only, "mix.ind" for serum + peptide mixture, and "err.ind" for the bad spot.
Samples were randomly assigned to spots on the plate and this matrix decodes the positions of the various samples/concentrations/replicates. The column headings of "dir.org" are:
Dilution2005Raw
An object of msSet
. See msSet
in package msProcess
for details.
Randolph TW and Yasui Y, ``Multiscale processing of mass spectrometry data," Biometrics, 62:589–597, 2006.
Randolph TW, Mitchell BL, McLerran DF, Lampe PD, and Feng Z, ``Quantifying peptide signal in MALDI-TOF mass spectrometry data," Molecular and Cellular Proteomics, 4(12):1990–1999, 2005.
Randolph TW, ``Scale-based normalization of spectral data," Cancer Biomarkers, 2(3–4):135-144, 2006.
data(Dilution2005Raw, package="msDilution") ## illustration of how to get the indices for ## various types of samples dir.org <- Dilution2005Raw$coding$dir.org ## order the indices based on "Serum", "Conc", ## "Replicate", and "Manual" dir.ind <- order(dir.org[, "Serum"], dir.org[, "Conc"], dir.org[, "Replicate"], dir.org[, "Manual"]) ## get the ordered indices dir.ord <- dir.org[dir.ind,] ## index for cytochrome c cyt.ind <- dir.ord[dir.ord[,"Serum"]==6, "Index"] ## indices for peptide mixture pep.ind <- dir.ord[dir.ord[,"Serum"]==0, "Index"] ## indices for serum-only ser.ind <- dir.ord[dir.ord[,"Serum"]!=6 & dir.ord[,"Conc"]==0, "Index"] ## indices for serum + peptide mixture mix.ind <- dir.ord[dir.ord[,"Serum"] %in% 1:5 & dir.ord[,"Conc"]!=0, "Index"] ## index for the bad spot (serum 1, concentration ## 6, replicate 4 + serum 4, concentration 0, ## replicate 1) err.ind <- dir.ord[dir.ord[,"Serum"]==1 & dir.ord[,"Conc"]==6 & dir.ord[,"Replicate"]==4, "Index"]