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())
MArrayLM
, i.e.\ the output of the functions
eBayes
and lmFit
from the limma package.coef
of the function topTable
in limma.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
.samControl
for these arguments, which should only be changed if they are fully understood.ebamControl
for these arguments, which should only be changed if their meaning is fully understood.SAM
or EBAM
.
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