sam.lambda {siggenes}R Documentation

Further SAM analysis

Description

If the output of a previous analysis with sam was assigned to a vector, this function can be used to compute the number of significant genes and the FDR for values of the threshold Delta that was not used in the previous analysis.

Usage

sam.lambda(sam.out,delta)

Arguments

sam.out the object to which the output of a previous analysis with sam was assigned.
delta vector of values for the threshold Delta.

Value

a table of statistics (estimate for p0, number of significant genes, number of falsely called genes and FDR) for the specified set of Deltas.

Note

This function can only be used for a SAM analysis – not for a SAM.Wilc analysis.

SAM was introduced by Tusher et al. (2001).

!!! There is a patent pending for the SAM technology at Stanford University. !!!

Author(s)

Holger Schwender, holger.schw@gmx.de

References

Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response, PNAS, 98, 5116-5121.

Schwender, H. (2003). Assessing the False Discovery Rate in a Statistical Analysis of Gene Expression Data, Chapter 5, Diploma thesis, Department of Statistics, University of Dortmund, http://de.geocities.com/holgerschw/thesis.pdf.

See Also

sam.plot sam sam.wilc


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