addonPreprocessing {compdiagTools} | R Documentation |
Compute expression levels for a single new chip similar to
runPreprocessing
using the scale
information stored by that function.
addonPreprocessing(BASEPATH, COVDESC = file.path(BASEPATH, "celfiles_addon.lst"), EXPRSET = file.path(BASEPATH, "expression_set.rdat"), plot.preprocessing = TRUE)
BASEPATH |
Project path |
COVDESC |
Path to text-file containing complete paths to addon Affymetrix .CEL-files, names of samples and optional covariates |
EXPRSET |
where to write the expression set containing the preprocessed data and corresponding documentation. |
plot.preprocessing |
Logical value if quality-plots should be prepared |
This function performs addon preprocessing according to the
runPreprocessing
method. It uses the scle information stored by
that function in order to normalize the celfiles found in the
COVDESC
file accordingly. The expression levels are added to
the expression set and rank-residual plots as well as the
residual-location plots are generated for the samples provided. The
method relies on the docval package for this task and uses vsn as well
as median polish for the computing of expression levels.
Logical value if preprocessing finished correctely
Claudio Lottaz