arrayQualityMetrics {arrayQualityMetrics} | R Documentation |
arrayQualityMetrics
performs quality metrics on
ExpressionSet
,
AffyBatch
,
NChannelSet
,
BeadLevelList
,
RGList
,
MAList
,
marrayRaw
or
marrayNorm
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, intgroup, grouprep) arrayQualityMetrics(expressionset, outdir = getwd(), force = FALSE, do.logtransform = FALSE, split.plots = FALSE, intgroup = "Covariate", grouprep = FALSE) ## S4 method for signature 'AffyBatch': arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots, intgroup, grouprep) ## S4 method for signature 'NChannelSet': arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots, intgroup, grouprep) ## S4 method for signature 'BeadLevelList': arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots, intgroup, grouprep) ## S4 method for signature 'RGList': arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots, intgroup, grouprep) ## S4 method for signature 'MAList': arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots, intgroup, grouprep) ## S4 method for signature 'marrayRaw': arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots, intgroup, grouprep) ## S4 method for signature 'marrayNorm': arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots, intgroup, grouprep)
expressionset |
is an object of
class ExpressionSet ,
AffyBatch ,
NChannelSet ,
BeadLevelList ,
RGList ,
MAList ,
marrayRaw or
marrayNorm . |
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. |
intgroup |
Name of the column of the phenoData to be used to draw a color side bar next to the heatmap. |
grouprep |
Decide if you want the boxplots and density plots to be coloured function of the groups set by 'intgroup'. The default is FALSE meaning that the boxplot and density plots will not be represented function of the groups of 'intgroup'. |
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) # "QMreport.html" is a report created in the "MLL" directory # on the logarithm expression data of the MLL.A AffyBatch. # 10 experiments are represented by density plots. ## End(Not run)