IBSpectra preprocessing

Description

Preprocessing is a necessary step prior to analysis of data. In a sequential order, it is often neccassary to correct isotope impurities, to normalize, and subtract additive noise.

Isotope impurity correction

correctIsotopeImpurities(x):

Returns impurity corrected IBSpectra object by solving a linear system of equations. See also isotopeImpurities.

Normalization

normalize(x,f=median,target="intensity",exclude.protein=NULL, use.protein=NULL,f.doapply=TRUE,log=TRUE,channels=NULL,na.rm=FALSE):

Normalizes the intensities for multiplicative errors. Those changes are most likely produced by pipetting errors, and different hybridization efficencies, but can also be due to biological reasons. By default, tag intensities are multiplied by a factor so that the median intensity is equal across tags.

f:

f is applied to each column, unless f.doapply is FALSE. Then f is supposed to compute column-wise statistics of the matrix of intensities. E.g. colSums and colMeans.

target:

One of "intensity" and "ratio".

exclude.proteins

Spectra of peptides which might come from these proteins are excluded. Use for example for contaminants and proteins depleted in the experiment.

use.protein:

If specified, only spectra coming from this protein are used. Use when a protein is spiked-in as normalization control.

f.isglobal:

If true, f is applied on each column. If false, f is supposed to compute column-wise statistics of the matrix of intensities. E.g. colSums and colMeans.

log:

Used when target=ratio.

Substract additive noise

subtractAdditiveNoise(x,method="quantile",shared=TRUE,prob=0.01):

method

'quantile' method is supported for now. It take's the prob (0.01) quantile to estimate the noise level. This value is subtracted from all intensities, and all remaining intensities have to be at least that value.

prob

See 'method'.

shared

If channels are assumed similar in intensity and hence a shared noise level is reasonable. If not, then one level per channel is necessary.

Exclusion of proteins

exclude(x,proteins.to.exclude):

Removes spectra which are assigned to proteins in protein.to.exclude from the object. This can be useful to remove contaminants. It create a new grouping based on the data which is left.

proteins.to.exclude

Proteins to exclude.

Author(s)

Florian P. Breitwieser, Jacques Colinge

See Also

ProteinGroup, IBSpectra, isobar-analysis, isobar-plots

Examples

data(ibspiked_set1)
maplot(ibspiked_set1,main="IBSpiked, not normalized")
maplot(normalize(ibspiked_set1),main="IBSpiked, normalized")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(isobar)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to isobar (v 1.18.0)
   'openVignette("isobar")' and '?isobar' provide help on usage.


Attaching package: 'isobar'

The following object is masked from 'package:BiocGenerics':

    normalize

The following object is masked from 'package:base':

    paste0

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/isobar/isobar-preprocessing.Rd_%03d_medium.png", width=480, height=480)
> ### Name: isobar-preprocessing
> ### Title: IBSpectra preprocessing
> ### Aliases: isobar-preprocessing correctIsotopeImpurities
> ###   correctIsotopeImpurities,IBSpectra-method normalize
> ###   subtractAdditiveNoise subtractAdditiveNoise,IBSpectra-method exclude
> ###   exclude,IBSpectra,character-method
> 
> ### ** Examples
> 
> data(ibspiked_set1)
> maplot(ibspiked_set1,main="IBSpiked, not normalized")
> maplot(normalize(ibspiked_set1),main="IBSpiked, normalized")
LOG: is.normalized: TRUE
	normalizing ibspiked_set1.ibspectra.csv [14991 spectra]
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 114: 0.8177
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 115: 0.9634
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 116: 1
LOG: normalization.multiplicative.factor file ibspiked_set1.ibspectra.csv channel 117: 0.9961
Warning message:
In normalize(ibspiked_set1) :
  Isotope impurity correction has not been logged - data might be uncorrected. See ?correctIsotopeImpurities.
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>