boxplt.cpd {compdiagTools}R Documentation

Boxplot of Expression Levels

Description

Draws a boxplot for each chip given in a gene expression matrix or standard errors given in plmset-object

Usage

boxplt.cpd(fr, filename = NULL, pointsize = 14, height = 1.6 + ncol(fr) * pointsize/48, 
           call = "", ...)
boxplt.plmset.cpd(plmset, filename = NULL, pointsize = 14, 
                  height = 1.6 + ncol(coefs(plmset)) * pointsize/48, ...)

Arguments

fr a gene expression matrix.
plmset affyPLM-object of which standard error estimates are extracted.
filename store a bitmap/pdf here is this argument is specified.
pointsize gives the font size
height height in inches
call either 'summary' or 'normalized'
... further arguments passed to bitmap command for writing files.

Details

Draws a boxplot of gene expression levesl after summary or after normalization. Given the hypothesis that gene expression levels are distributed simmilarly across chips from the same experiment, we want to see similar boxplots as well.

boxplt.plmset.cpd does the same for estimated standard errors on the residuals. We want to see low residuals, because this means that the fitting of the linear model went fine.

Note

Use type="pdfwrite" as parameter to generate PDF

Author(s)

Stefan Bentink

See Also

bitmap

Examples

library(golubEsets)
data(golubTest)
expr.mat <- exprs(vsn(golubTest, describe.preprocessing=FALSE))
boxplt.cpd(expr.mat)

[Package compdiagTools version 1.5.3 Index]