computeSFandSDT {sscore} | R Documentation |
Computes the scaling factor (SF) and statistical difference threshold (SDT) values of Affymetrix GeneChips, for use in calculating S-Score values
computeSFandSDT(afbatch, TGT = 500, digits = NULL, verbose = FALSE, plot.histogram = FALSE, celfile.path = NULL)
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 |
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) }