Description Slots Methods Author(s) References

An object returned from a call to GetStabilityOverlap.

`intersection`

: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 row

`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 ranking procedures.`overlapscore`

:A matrix of overlap scores, arranged analogously to

`intersection`

.`noinformation`

:A list containing two numeric vectors named

`"intersection"`

and`"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.`scheme`

s. GetStabilityOverlap.

`decay`

The decay scheme used for the weights, s. GetStabilityOverlap.

- show
Use

`show(object)`

for brief information.- summary
Use

`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`display`

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`scheme`

.- plot
`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`1`

to`frac*number of genes`

. The argument mode specifies whether this is done as average over all lists (`mode = "mean"`

), for a certain alternative list`which`

(`mode = "specific"`

) or succesively in the form of separate plots for each alternative list (`mode = "all"`

). The`...`

argument may be used to modify graphical options.

Martin Slawski

Anne-Laure Boulesteix

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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