Entering edit mode
Hi,
I was asked the question today, if the 'logcounts' you get from running logNormCounts with defaults gives you log2 normalised counts. I assumed yes but I thought I should double check.
I looked at the documentation and it would indicate in the transform argument that the default is to use log.
When I look in the documentation for log() I see that the default is e.
I thought this didn't seem right so I ran a quick test comparing the outputs and it seems that logNormCounts does actually return log2 normalised counts as I originally assumed.
Unless I have completely misunderstood something is the documentation potentially misleading?
Sorry, I was confused. It says the default for transform is log but the default for log is e in the documentation for logNormCounts. I didn't go through to normalizeCounts.
It's log2. See ?logNormCounts. Everything in bioinformatics is typically log with base 2.