BeadSummaryList-class {beadarray} | R Documentation |
A list based class for storing bead summary data. BeadSummaryList
objects can be created from BeadLevelList
objects or by reading
directly from pre-processed BeadStudio output by using the readBeadSummaryData
function.
Objects should contain the following list components:
R : | Numeric matrix containing foreground intensites for the red channel. Rows correspond to beadtypes and columns to arrays. |
Rb : | Numeric matrix containing background intensites for the red channel. |
BeadStDev : | Standard deviations for each bead type per array. |
NoBeads : | Number of beads of each type per array. |
ProbeID : | ID for each probe on the arrays. |
nooutliers : | The number of beads flagged as outliers for each bead type per array. This is only used for bead summary data created by beadarray and not for pre-processed data read from BeadStudio |
BeadSummaryLists
can be subsetted and combined. They also return dimensions
so functions such asdim
, nrow
and ncol
are also defined. BeadSummaryList
uses an adapted version of the show
method from the Limma class LargeDataObject
. This
means that the BeadSummaryList
will print in a relatively compact way.
Other functions which operate on BeadSummaryList
objects include:
plotXY.beads
plotMA.beads
getMeanIntensities
pairwiseMA
Mark Dunning and Mike Smith