aqmobj.prepdata-class {arrayQualityMetrics} | R Documentation |
Class to contain data generated from aqm.prepdata.
Description
Container for the output of aqm.prepdata
and
for the input of the aqm functions.
Details
See the aqm.prepdata help or the aqm Vignette for example of this object.
Slots
M
:- A matrix of the M values (log-ratio). The
log-ratio is computed with the second channel being the median of the
intensities across arrays in the case of one channel arrays.
A
:- A matrix of the A values. The A value is the mean
of the two intensities. The second channel is computed as for the M
values in the case of one channel arrays.
dat
:- A matrix with the log-ratio if two channels or
the intensities if one channel.
rc
:- A matrix with the red channel intensities in the
case of two channels arrays.
gc
:- A matrix with the green channel intensities in the
case of two channels arrays.
rcb
:- A matrix with the red channel background
intensities if two channels arrays and if available.
gcb
:- A matrix with the green channel background
intensities if two channels arrays and if available.
outM
:- The distance between each pairs of arrays,
computed using
dist2
from the
genefilter
package.
sN
:- Integers numbering the arrays to be used to label
the plots.
numArrays
:- An integer giving the number of arrays.
nchannels
:- A numeric giving the number of channels.
logtransformed
:- A logical telling if the data have
been log transformed by the function aqm.prepdata.
classori
:- A character string of the class of the
object that was given as an input of the aqm.prepdata function.
Author(s)
Audrey Kauffmann <audrey@ebi.ac.uk>
See Also
aqm.prepdata
, aqm.boxplot
, aqm.density
, aqm.heatmap
, aqm.maplot
, aqm.meansd
, aqm.probesmap
, aqm.spatial
, aqm.spatialbg
[Package
arrayQualityMetrics version 2.2.3
Index]