limma2sam {siggenes} | R Documentation |
Transforms the output of an analysis with limma into a SAM
or EBAM
object, such that a SAM or EBAM analysis, respectively,
can be performed using the test statistics provided by limma.
limma2sam(fit, coef, moderate = TRUE, sam.control = samControl()) limma2ebam(fit, coef, moderate = TRUE, delta = 0.9, ebam.control = ebamControl())
fit |
an object of class MArrayLM , i.e. the output of the functions
eBayes and lmFit from the limma package. |
coef |
column number or name corresponding to the coefficient or contrast of
interest. For details, see the argument coef of the function topTable
in limma. |
moderate |
should the limma t-statistic be considered? If FALSE , the
ordinary t-statistic is used in the trasnsformation to a SAM or EBAM
object. If TRUE , it is expected that fit is the output of eBayes .
Otherwise, fit can be the result of lmFit or eBayes . |
sam.control |
further arguments for the SAM analysis. See samControl
for these arguments, which should only be changed if they are fully understood. |
delta |
the minimum posterior probability for a gene to be called differentially
expressed (or more generally, for a variable to be called significant) in an EBAM
analysis. For details, see ebam . Please note that the meaning of
delta differs substantially between sam and ebam |
ebam.control |
further arguments for an EBAM analysis. See ebamControl
for these arguments, which should only be changed if their meaning is fully understood. |
An object of class SAM
or EBAM
.
Holger Schwender, holger.schwender@udo.edu
Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment. JASA, 96, 1151-1160.
Smyth, G.K. (2004). Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Statistical Applications in Genetics and Molecular Biology, 3(1), Article 3.
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance Analysis of Microarrays Applied to the Ionizing Radiation Response. PNAS, 98, 5116-5121.
sam
, ebam
, SAM-class
, EBAM-class
,
samControl
, ebamControl