sscore (version 1.44.0)

computeSFandSDT: Compute SF and SDT values

Description

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

Usage

computeSFandSDT(afbatch, TGT = 500, digits = NULL, verbose = FALSE, plot.histogram = FALSE, celfile.path = NULL)

Arguments

afbatch

An AffyBatch object

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

celfile.path

character denoting the path for the *.CEL files corresponding to afbatch

Value

returns a list containing the following components:

SF

SF values, one for each GeneChip

SDT

SDT values, one for each GeneChip

Details

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.

References

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

Examples

  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)

}