jmacdon / affycoretools

affycoretools

Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools.

The affycoretools package is primarily intended to make analyses of Affymetrix GeneChip data simpler and more straightforward. There are any number of packages designed for preprocessing or analyzing Affy data, but there are not so many that help streamline the analysis to help create useful output that can be given to collaborators.

The affycoretools package is also intended to be used as a way to do reproducible research, where the analysis and documentation are all held in a single file, that is then processed by R to create the output data, as well as a nicely formatted pdf that documents the analysis. The affycoretools package can be used with either Sweave or knitr documents, although these days knitr is really the way to go.

In addition, affycoretools can be used with either annaffy or ReportingTools to create useful output in HTML or text format to share with your collaborators. However, ReportingTools is being actively developed and maintained, whereas annaffy is not, so the intention is to slowly convert all the functions to primarily use ReportingTools.

affycoretools's Issues

affycoretools::plotPCA() accepts cex arguement for point size but reports error "unused argument (cex = 2)"

When plotting PCA plot for a ExpressionSet object using

affycoretools::plotPCA(eset, cex = 2)

it works and produces a PCA plot with point size 2 as expected, but it reports:

Error in pca.legend(pca, groups, groupnames, plotstuff, x.coord = x.coord,  : 
  unused argument (cex = 2)

at the same time.