SScore {sscore}R Documentation

Compute S-Score values

Description

Computes the S-Score values for a pair of Affymetrix GeneChips

Usage

SScore(afbatch = stop("No CEL files specified"), SF = NULL, SDT = NULL, 
       rm.outliers = TRUE, rm.mask = TRUE, rm.extra = TRUE, 
       digits = NULL, verbose = FALSE, celfile.path = NULL, celfile.names = NULL)

Arguments

afbatch An AffyBatch object
SF a list of Scale Factor (SF) values for each GeneChip
SDT a list of Standard Difference Threshold (SDT) values for each GeneChip
rm.outliers should the spots marked as 'OUTLIERS' be excluded from S-Score calculation?
rm.mask should the spots marked as 'MASKS' be excluded from S-Score calculation?
rm.extra if TRUE, overrides what is in rm.mask and rm.outliers
digits number of significant digits for S-Score values
verbose logical value. If TRUE it provides more detail of the S-Score calculations.
celfile.path character denoting the path for the *.CEL files corresponding to afbatch
celfile.names optional character vector containing the names of the *.CEL files

Details

Computes S-Score values as described by Zhang et al. (2002). SScore provides a simpler interface when comparing only two GeneChips, while SScoreBatch allows comparison of multiple pairs of chips.

The SF and SDT factors are required for all calculations. If NULL, these values will be calculated according to the Affymetrix Statistical Algorithms Description Document. digits allows the specification of the number of significant digits for the S-Score values; if NULL, the maximum number of significant digits are retained.

Value

An exprSet with S-Score values in the exprs slot and CorrDiff values in the se.exprs.

Note

Based on C++ code by Li Zhang and Delphi code by Robnet Kerns

Author(s)

Richard Kennedy rkennedy@vcu.edu

References

Zhang, L., Wang, L., Ravindranathan, A., Miles, M.F. (2002) A new algorithm for analysis of oligonucleotide arrays: application to expression profiling in mouse brain regions. Journal of Molecular Biology, 317(2), pp. 225–35

Kerns, R.T., Zhang, L., Miles, M.F. (2003) Application of the S-score algorithm for analysis of oligonucleotide microarrays. Methods, 31(4), pp. 274–81

See Also

SScoreBatch,computeSFandSDT,computeOutlier

Examples

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

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

  ## default calling method
  SScores <- SScore(abatch)

  ## specifying SF and SDT (gives same results as above)
  SfSdt <- computeSFandSDT(abatch)
  SScores <- SScore(abatch,SF=SfSdt$SF,SDT=SfSdt$SDT)

  ## specifying outlier and masked values should be included in calculations
  SScores <- SScore(abatch,rm.outliers=FALSE,rm.mask=FALSE)

  ## round results to 3 significant digits
  SScores <- SScore(abatch,digits=3)

  ## show verbose output
  SScores <- SScore(abatch,verbose=TRUE)

}


[Package sscore version 1.6.0 Index]