Is logNormCounts log2 normalised counts as default?
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@3e647591
Last seen 14 months ago
United Kingdom

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?

scuttle scater • 1.6k views
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@alanocallaghan-14291
Last seen 5 months ago
United Kingdom

The documentation for ?normalizeCounts indicates it is indeed log2 normalisation

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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.

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It's log2. See ?logNormCounts. Everything in bioinformatics is typically log with base 2.

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