normalizeArray: Normalize tiling array data using sequence information

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/normalizeArray.R

Description

This function is used to normalize the peptide microarray data using sequence information.

Usage

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normalizeArray(peptideSet, method = "ZpepQuad", robust = TRUE,
  centered = TRUE)

Arguments

peptideSet

A peptideSet. The expression data for the peptides as well as annotations and ranges.

method

A character. The normalization method to be used. Can be "Zpep" or "ZpepQuad".

robust

A logical. If TRUE, reweigthed least-squares estimates are computed.

centered

A logical. If TRUE, recenter the data.

Details

The available methods are "Zpep" and "ZpepQuad". These methods fit a linear model using either linear or linear and quadratic terms (respectively), regressing intensity on the peptides' five Z-scale scores. A peptide Z-scale score is obtained by summing over the Z-scale values in Sandburg et al (1998) of the amino acids the peptide comprises.

Peptide Z-scale scores may be provided in the featureRange slot of peptideSet. This slot is a GRanges object x, and the function will seek five columns labelled z1 through z5 in values(x). If these are not found, the function attempts to calculate Z-scales from sequence information found in peptide(peptideSet)

If robust = TRUE the linear model is fit with t_4 distributed errors. The method returns the residuals of each peptide intensity in the fitted linear model. If centered = TRUE the fitted intercept term is added back to the residuals of the fit.

Value

A peptideSet object with updated normalized intensity values.

Author(s)

Raphael Gottardo, Gregory Imholte

References

Sandberg, M., Eriksson, L., Jonsson, J., Sjostrom, M., and Wold, S. (1998). New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. Journal of Medicinal Chemistry 41, 2481-2491.

See Also

summarizePeptides, makeCalls

Examples

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## This example curated from the vignette -- please see vignette("pepStat")
## for more information
if (require("pepDat")) {

  ## Get example GPR files + associated mapping file
  dirToParse <- system.file("extdata/gpr_samples", package = "pepDat")
  mapFile <- system.file("extdata/mapping.csv", package = "pepDat")

  ## Make a peptide set
  pSet <- makePeptideSet(files = NULL, path = dirToParse,
                         mapping.file = mapFile, log=TRUE)

  ## Plot array images -- useful for quality control
  plotArrayImage(pSet, array.index = 1)
  plotArrayResiduals(pSet, array.index = 1, smooth = TRUE)

  ## Summarize peptides, using pep_hxb2 as the position database
  data(pep_hxb2)
  psSet <- summarizePeptides(pSet, summary = "mean", position = pep_hxb2)

  ## Normalize the peptide set
  pnSet <- normalizeArray(psSet)

  ## Smooth
  psmSet <- slidingMean(pnSet, width = 9)

  ## Make calls
  calls <- makeCalls(psmSet, freq = TRUE, group = "treatment",
                     cutoff = .1, method = "FDR", verbose = TRUE)

  ## Produce a summary of the results
  summary <- restab(psmSet, calls)

}

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

No methods found in "GenomicRanges" for requests: mcols<-
No methods found in "GenomicRanges" for requests: mcols
Loading required package: pepDat
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'pepDat'

pepStat documentation built on Nov. 8, 2020, 6:45 p.m.