spkMA {spkTools} | R Documentation |
Plots log-ratios (M) vs. average log expression (A) for a SpikeInExpressionSet object.
spkMA(object, spkSlopeOut, fc=2, tol=3, label=NULL, ylim=NULL, outlier=1, reduce=TRUE, plot.legend=TRUE)
object |
a SpikeInExpressionSet object |
spkSlopeOut |
the output from the spkSlope function |
fc |
the fold change of interest |
tol |
the precision (number of digits after decimal point) in fc |
label |
a character string to insert into the plot title |
ylim |
limits of y-axis |
outlier |
log fold change cut-off for outliers |
reduce |
if TRUE some points are removed from the background to speed plotting |
plot.legend |
if TRUE a legend is plotted |
The MA plot is produced.
Matthew N. McCall
data(affy) affySlope <- spkSlope(affy) spkMA(affy, affySlope)