plateEffects {cellHTS2} | R Documentation |
This generic function accesses plate effects stored in slot rowcol.effects
and overall.effects
of a cellHTS
instance.
plateEffects(object)
object |
Object derived from class cellHTS that has been normalized by a spatial normalization method. See details. |
plateEffects
returns a list with two elements: rowcol
and overall
.
plateEffects[["rowcol"]]
corresponds to the contents of slot rowcol.effects
of object
. This is a 3D array with the same dimensions as Data(object)
: nr of Features x nr of Samples x nr of Channels
of the current cellHTS
object.
plateEffects[["overall"]]
contains the data stored in slot overall.effects
of object
. This is a 3D array with dimensions nr Plates x nr Samples x nr Channels
of object
. Slot overall.effects
is only estimated when B score method is used to normalize the data.
Note that these 2 slots accessed by this function were stored after preprocessing the data either using Bscore method or local regression fit (see normalizePlates
for details), by setting the option save.model=TRUE
.
Ligia Bras ligia@ebi.ac.uk
cellHTS
normalizePlates
Bscore
spatialNormalization