SScore {sscore} | R Documentation |
Computes the S-Score values for a pair of Affymetrix GeneChips
SScore(afbatch = stop("No CEL files specified"), classlabel = c(0,1), SF = NULL, SDT = NULL, rm.outliers = TRUE, rm.mask = TRUE, rm.extra = NULL, digits = NULL, verbose = FALSE, celfile.path = NULL, celfile.names = NULL)
afbatch |
An AffyBatch object |
classlabel |
A vector identifying the class for each column of the 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 |
Computes S-Score values as described by Zhang et al. (2002). SScore
provides a simpler
interface for comparing only two classes of GeneChips, while SScoreBatch
compares
multiple pairs of chips.
The classlabel consists of a vector with one entry for each column of the AffyBatch
object.
Each entry consists of a 0 or a 1 to identify the class to which the chip for the corresponding column
belongs. SScore
will conduct a two-class test comparing all chips labeled 0 to all chips
labeled 1. If classlabel is not specified, it defaults to a two-chip comparison, compatible with
previous versions of SScore
.
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.
An ExpressionSet
with S-Score values in the exprs
slot.
Based on C++ code by Li Zhang and Delphi code by Robnet Kerns
Richard Kennedy rkennedy@vcu.edu
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
SScoreBatch
,computeSFandSDT
,computeOutlier
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) }