hi Sophie,

The transformations in DESeq and DESeq2 are log2-like transformations. If
the expected count is between 0 and 1, the values can be negative, this
does not indicate a problem.

Mike


On Sun, Apr 13, 2014 at 5:17 PM, Sophie Josephine Weiss <
Sophie.Weiss@colorado.edu> wrote:

> Hello,
> I have microbiome data with no replicates, from different conditions.  I am
> trying to transform the data using the DESeq method, as described in
> McMurdie and Holmes 2014.
>
> The attached file is the definition I am using, as per the supplemental
> info in McMurdie and Holmes 2014, and the .biom file I am using.
>
> Thank you for your help,
> Sophie
>
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