LEMMA {lemma}R Documentation

Laplace approximated EM Microarray Analysis

Description

LEMMA fits a linear mixed model to normalized microarray data. See the complete LEMMA paper (on the lemma web site) which contains the underlying model and the theory.

http://www.stat.cornell.edu/lemma/docs/LEMMAsummary.pdf contains a short summary of the model.

This version supports two treatment groups and either a two-way classification (null and nonnull genes, as in the LEMMA paper), or a three-way classification: null genes, for which statistically there is no difference in expression between the two treatment groups; nonnull group 1 - genes that are significantly more expressed in treatment group 1 than in treatment group 2; and nonnull group 2 - genes that are significantly more expressed in treatment group 2 than in treatment group 1.

The program runs on both Windows and Linux.

Details

The input should consist of a data frame with G rows, and have the following structure:

In this version n1 and n2 do not have to be the same, but all the rows in Y1 have to have n1 elements, and all the rows in Y2 have to have n2 elements. The program also uses the following variables when the user invokes the lemma function: outdir, locfdrcutoff, fdrcutoff, topgenes, titletext, mgq, tol, maxIts, modes, plots.

All of the parameter estimates, plots, and gene lists will be saved under the outdir directory. In particular, this directory will contain the following files:

Note:

Author(s)

Bar, H.Y. hyb2@cornell.edu, Schifano, E.D. eds27@cornell.edu

References

Bar, H.Y., Booth, J.G., Schifano, E.D., Wells, M.T., (2009). Laplace approximated EM Microarray Analysis: an empirical Bayes approach for comparative microarray experiments.

http://www.stat.cornell.edu/lemma/docs/lemma.pdf

See Also

Read lemma to see how to execute the program.

Use lemmaPlots to produce diagnostics plots.

Use printTopGenes to produce a list of genes sorted by their adjusted p-values or by their posterior null probabilities.

Examples

## Not run: 
lemma(apoai,titletext="APO-AI, Callow et al (2000)",outdir="OUT/apoai",
   plots=F)
lemmaPlots("OUT/apoai",mgq=0.99, titletext="APO-AI (Callow et al., 2000)")

lemma(simdata,titletext="Simulated data",outdir="OUT/simdata")

# Similarly, if the user wants to use the 2-way classification:
lemma(apoai,titletext="APO-AI, Callow et al (2000)",outdir="OUT/apoai",
  modes=2, plots=F)
lemmaPlots("OUT/apoai",mgq=0.99,titletext="APO-AI (Callow et al., 2000)",
      modes=2)

## End(Not run)

[Package lemma version 1.2-1 Index]