An object returned from a call to GetStabilityOverlap.
A matrix of intersection counts, normalized such that 1 is the maximum attainable value. The rows
correspond to the positions in the list such that
i contains the number of common elements
of two lists up to position
i. The columns correspond to lists,
either obtained from altered datasets or by applying multiple
A matrix of overlap scores, arranged analogously to
A list containing two numeric vectors named
"overlap score" containing for each list position intersection counts and overlap scores
one would expect in the no-information case, corresponding to the random generation of
two mutually independent lists.
The decay scheme used for the weights, s. GetStabilityOverlap.
show(object) for brief information.
summary(object), measure = c("overlapscore", "intersection"), display = c("summary", "all"), position, digits = 3 for
condensed output. The argument
measure specifies the measure one is interested in. The argument
controls whether only a five-point summary is printed (
display = "summary") or whether all results
are printed (
display = "all"). The argument
position specifies the list position, e.g. if
position = 10, then
intersection counts/overlap scores up to position 10 are summarized. The argument
digits is used for number
formatting. Note that the output depends on
plot(object, frac=1/50, mode = c("mean", "all", "specific"), which = 1, ...) produces a graphical display
of the intersection count (upper panel) and the overlap score (lower panel) for increasing list position, ranging from
frac*number of genes. The argument mode specifies whether this is done as average over all
mode = "mean"), for a certain alternative list
mode = "specific") or
succesively in the form of separate plots for each alternative list (
mode = "all"). The
... argument may be used to modify
Qiu, X., Xiao, Y., Gordon, A., Yakovlev, A., (2006)
Assessing stability of gene selection in microarray data analysis. BMC Bioinformatics 7, 50
Yang, X., Bentink, S., Scheid, S., Spang, R. (2006)
Similarities of ordered gene lists. Journal of Bioinformatics and Computational Biology 4, 693-708
Lottaz, C., Yang, X., Scheid, S., Spang, R. (2006)
OrderedList - a Bioconductor package for detecting similarity in ordered gene lists. Bioinformatics, 22, 2315-2316
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