[BioC] problem with lumiR.batch log2 transformation

[Briggs, Chris]

As a novice Bioconductor/R user, I have a question regarding log2 transformation and density plots. I want to look at how log2 transformation changes the density plot of expression data so I read in my data without log2 transformation:

x <- lumiR.batch ("CP27_M8_SAMPLE PROBE PROFILE_NO NORM_080511.txt",transform='none')

density(x)

A Summary of file x shows what look like log2 transformed values and the x-axis of the plot is called 'log2 intensity' whereas if I apply log2 transformation, the Summary shows similar, but not identical, values and the plot looks the same except the x-axis is called 'intensity'

x <- lumiR.batch ("CP27_M8_SAMPLE PROBE PROFILE_NO NORM_080511.txt",transform='log2')

density(x)

What's going on?

Chris Briggs (Tufts Center for Neuroscience Research-Comp Genomics Core)