assessSpikeIn {affycomp} | R Documentation |
These functions are assessment functions.
Each takes an
ExpressionSet-class
and returns a list with necessary
information to create assessment plots.
assessSpikeIn(s,method.name=NULL,verbose=TRUE) assessMA(exprset,method.name=NULL) assessSignal(exprset,method.name=NULL) assessFC(exprset,method.name=NULL) assessFC2(exprset,method.name=NULL)
s |
An ExpressionSet-class containing
expression measures for Affymetrix's spike-in experiment. |
exprset |
An ExpressionSet-class containing
expression measures for Affymetrix's spike-in experiment. |
method.name |
Name of expression measure being assessed. |
verbose |
logical. If TRUE show messages. |
assessMA
performs the assessment for the MA-plot (Figure 1),
assessSignal
performs the assessment for signal detection plot
(Figure 4a), assessFC
performs assessments used by fold-change
related plots (Figures 5a, 6a, 6b). assessFC2
is for the ROC
for genes with nominal fold changes of 2 (Figure
5b). assessSpikeIn
is a wrapper for all these and returns a list
of lists.
Lists with the necessary information to make the Figures.
Rafael A. Irizarry