SScoreBatch {sscore} | R Documentation |
Computes the S-Score values for multiple pairs of Affymetrix GeneChips
SScoreBatch(afbatch = stop("No CEL files specified"), compare = stop("No list of comparisons given"), 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 |
compare |
A matrix describing which chips to compare |
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). SScoreBatch
allows comparison
of multiple pairs of chips, while SScore
provides a simpler interface when comparing only
two GeneChips.
compare
specifies how the pairwise comparisons are performed. It is an N x 2 matrix,
where N is the number of pairwise comparisons; each row of the matrix contains index in the AffyBatch
object
for the chips to be compared. For example,
1 3 4 2 5 9 10 2 5 7
would do a comparison of chip 1 to chip 3, a comparison of chip 4 to chip 2, a comparison of chip 5
to chip 9, and so on. The columns in ExpressionSet
correspond to the rows of compare
, so
that the results of the first comparison are in column 1, the results of the second comparison are
in column 2, and so on.
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.
probes. 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
SScore
,computeSFandSDT
,computeOutlier
if (length(dir(pattern=".cel$")) != 0) { ## Read in the *.CEL files abatch <- ReadAffy() ## default calling method SScores <- SScoreBatch(abatch) ## specifying SF and SDT (gives same results as above) SfSdt <- computeSFandSDT(abatch) ## specifying outlier and masked values should be included in calculations SScores <- SScoreBatch(abatch,SF=SfSdt$SF,SDT=SfSdt$SDT) SScores <- SScoreBatch(abatch,rm.outliers=FALSE,rm.mask=FALSE) ## round results to 3 significant digits SScores <- SScoreBatch(abatch,digits=3) ## show verbose output SScores <- SScoreBatch(abatch,verbose=TRUE) }