
Hi Mike-

Is there any reason NOT to convert the log2 counts back into expected counts using 2^(expected count after shrinking)? I want to avoid the negative values and by converting the data back into expected counts I can easily create relative abundance plots by calculating expected count for feature A in sample 1/total counts for all features in sample 1.

Thanks,
Kristina


On Jan 16, 2014, at 6:37 PM, Michael Love <michaelisaiahlove@gmail.com<mailto:michaelisaiahlove@gmail.com>> wrote:

On Thu, Jan 16, 2014 at 5:56 PM, Kristina M Fontanez <fontanez@mit.edu<mailto:fontanez@mit.edu>> wrote:
**I am including an earlier message which I neglected to cc to the Bioconductor forum, pasted below**

Mike-

Just one more short, related question - why is it that some of the rlogTransformed counts have negative values? I can certainly just add 1 to all of the values in order to make plotting relative abundance easier, but it seems strange that there should be negative values at all.


​rlog is the log2(expected count after shrinking), so if the expected count is between 0 and 1 you have a negative value.​





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Kristina Fontanez, Postdoctoral Fellow
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Massachusetts Institute of Technology
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