addonPreprocessing {compdiagTools}R Documentation

Incremental Preprocessing

Description

Compute expression levels for a single new chip similar to runPreprocessing using the scale information stored by that function.

Usage

addonPreprocessing(BASEPATH, COVDESC = file.path(BASEPATH, "celfiles_addon.lst"), 
                   EXPRSET = file.path(BASEPATH, "expression_set.rdat"), 
                   plot.preprocessing = TRUE)

Arguments

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

Details

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.

Value

Logical value if preprocessing finished correctely

Author(s)

Claudio Lottaz

See Also

runPreprocessing


[Package compdiagTools version 1.5.3 Index]