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]