computeAffxSFandSDT: Compute SF and SDT values using affxparser routines
In sscore: S-Score Algorithm for Affymetrix Oligonucleotide Microarrays

Description Usage Arguments Details Value Note Author(s) References Examples

View source: R/computeAffxSFandSDT.R

Computes the scaling factor (SF) and statistical difference threshold (SDT) values of Affymetrix GeneChips, for use in calculating S-Score values

1	computeAffxSFandSDT(afbatch, stdvs, pixels, TGT = 500, digits = NULL, verbose = FALSE, plot.histogram = FALSE)

`afbatch`	An `AffyBatch` object
`stdvs`	matrix of standard deviations for probe intensities from *.CEL file
`pixels`	matrix of number of pixels for probe intensities from *.CEL file
`TGT`	the target intensity to which the arrays should be scaled
`digits`	number of significant digits for SF and SDT values
`verbose`	logical value. If `TRUE` it provides more detail of the SF and SDT calculations.
`plot.histogram`	logical value. if `TRUE` it plots a histogram of intensities

Calculates SF and SDT factors using the algorithms described in the Affymetrix Statistical Algorithms Description Document. The SF and SDT may be used in the calculation of S-Score values, or may be useful in their own right. One SF and SDT value is calculated for each GeneChip, which are arranged in the same order as the columns in the AffyBatch object.

computeSFandSDT returns a list containing the following components:

`SF`	SF values, one for each GeneChip
`SDT`	SDT values, one for each GeneChip

Based on Affymetrix MAS5 Statistical SDK source code http://www.affymetrix.com/Auth/support/developer/stat_sdk/STAT_SDK_source.zip, as well as C++ code by Li Zhang and Delphi code by Robnet Kerns

Richard Kennedy rkennedy@vcu.edu

Affymetrix (2002) Statistical Algorithms Description Document, Affymetrix Inc., Santa Clara, CA, whitepaper. http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf

  if (length(dir(pattern=".cel$")) != 0) {

  ## Read in the *.CEL files
  abatch <- ReadAffy()

  ## compute SF and SDT
  SfSdt <- computeSFandSDT(abatch)

  ## show verbose output
  SfSdt <- computeSFandSDT(abatch,verbose=TRUE)

  ## plot PM and MM histograms for each *.CEL file
  SfSdt <- computeSFandSDT(abatch,plot.histogram=TRUE)

}