mas5 {affy} | R Documentation |
This function converts an instance of AffyBatch-class
into an instance of exprSet-class
using
our implementation of Affymetrix's MAS 5.0 expression measure.
mas5(object, normalize = TRUE, sc = 500, analysis = "absolute", ...)
object |
an instance of AffyBatch-class |
normalize |
logical. If TRUE scale normalization is used
after we obtain an instance of exprSet-class |
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
.
exprSet-class
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
data(affybatch.example) eset <- mas5(affybatch.example)