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)