runPreprocessing {compdiagTools} | R Documentation |
This function preprocesses a batch of Affymetrix .CEL-files. I.e., it checks the directory-structure, runs normalization and summary-statistics, produces diagnostic plots, and performs an Affymetrix-like quality control.
runPreprocessing(BASEPATH, COVDESC = paste(BASEPATH, "celfiles.lst", sep="/"), TMPPATH = "/scratch/local", EXPRSET = paste(BASEPATH, "expression_set.rdat", sep="/"), METHOD = "rma", plot.preprocessing = TRUE, run.simpleaffy = TRUE, cleanup.plmsets = TRUE)
BASEPATH |
Project path |
COVDESC |
Path to text-file containing complete paths to Affymetrix .CEL-files, names of samples and optional covariates |
TMPPATH |
Path to temporary directory for buffering
AffyBatch-class with raw-data in
it(default=/scratch/local/). |
EXPRSET |
where to write the expression set containing the preprocessed data and corresponding documentation. |
METHOD |
Method to be used for probeset summary ("rma" for medianpolish (default), other for affyPLM-method) |
plot.preprocessing |
Logical value if quality-plots should be prepared |
run.simpleaffy |
Logical value if Affymetrix
MAS5-quality-assessment should be performed
(qc ) |
cleanup.plmsets |
logical, TRUE if huge temporary data files are to be removed |
Under preparation
Logical value if preprocessing finished correctely
Stefan Bentink
under preparation
PLMset-class
,
AffyBatch-class
, qc