Finding Isoforms using Robust Multichip Analysis (FIRMA) based on .
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Additional arguments passed to
Returns a named
drop == FALSE, otherwise
FirmaSet object (containing the FIRMA scores).
It is strongly recommended to use a custom CDF, e.g. "core",
"extended" or "full" . To use a custom CDF, set it before
calling this method, i.e.
Do not set the standard "non-supported" Affymetrix CDF
(see also Section 'Flavors').
flavor == "v1b" (default), then the standard
"non-supported" Affymetrix CDF is used for background correction
and the quantile normalization steps, and the custom CDF
is used for the probe summarization and everything that follows.
The advantage of this flavor is that those two first preprocessing
steps will remain the same if one later changes to a different
flavor == "v1a", then the custom CDF is used throughout
all steps of FIRMA, which means that if one changes the custom CDF
all steps will be redone.
 E. Purdom, K. Simpson, M. Robinson, J. Conboy, A. Lapuk & T.P. Speed,
FIRMA: a method for detection of alternative splicing from
exon array data, Bioinformatics, 2008.
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