mas5 {affy} | R Documentation |
This function converts an instance of AffyBatch
into an instance of ExpressionSet
using
our implementation of Affymetrix's MAS 5.0 expression measure.
mas5(object, normalize = TRUE, sc = 500, analysis = "absolute", ...)
object |
an instance of AffyBatch |
normalize |
logical. If TRUE scale normalization is used
after we obtain an instance of ExpressionSet |
sc |
Value at which all arrays will be scaled to. |
analysis |
should we do absolute or comparison analysis, although "comparison" is still not implemented. |
... |
other arguments to be passed to expresso . |
This function is a wrapper for expresso
and
affy.scalevalue.exprSet
.
The methods used by this function were implemented based upon available documentation. In particular a useful reference is Statistical Algorithms Description Document by Affymetrix. Our implementation is based on what is written in the documentation and, as you might appreciate, there are places where the documentation is less than clear. This function does not give exactly the same results. All source code of our implementation is available. You are free to read it and suggest fixes.
For more information visit this URL: http://stat-www.berkeley.edu/users/bolstad/
expresso
,affy.scalevalue.exprSet
if (require(affydata)) { data(Dilution) eset <- mas5(Dilution) }