| arrayQualityMetrics {arrayQualityMetrics} | R Documentation |
arrayQualityMetrics performs quality metrics on
ExpressionSet,
AffyBatch or
NChannelSet containing
microarray data from any platforms, one or two channels. The results,
presented in a HTML report, are designated to allow the user
to rapidly assess the quality of a set of arrays.
## S4 method for signature 'ExpressionSet':
arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots)
arrayQualityMetrics(expressionset,
outdir = getwd(),
force = FALSE,
do.logtransform = FALSE,
split.plots = FALSE)
## S4 method for signature 'AffyBatch':
arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots)
## S4 method for signature 'NChannelSet':
arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots)
expressionset |
is an object of
class ExpressionSet,
AffyBatch or
NChannelSet. |
outdir |
is the name of the directory in which the results are created. |
force |
if TRUE, outdir will be overwritten if it
already exists. |
do.logtransform |
If TRUE, the data are log transformed before the analysis. |
split.plots |
If the number of studied array is more than 50 it is adviced to define a number of experiments to represent on the density plots. |
A directory outdir containing a HTML report named QMreport.html and all the PNG and PDF plots is created.
Audrey Kauffmann, Wolfgang Huber. Maintainer: <audrey@ebi.ac.uk>
## Not run:
library(ALLMLL)
data(MLL.A)
arrayQualityMetrics(expressionset = MLL.A,
outdir ="MLL",
do.logtransform = TRUE,
split.plots = 10)
# "MLL_QMreport.html" is a report created in the working directory
# on the logarithm expression data of the MLL.A AffyBatch.
# 10 experiments are represented by density plots.
## End(Not run)