[BioC] Can DESeq do this?

Michael Love michaelisaiahlove at gmail.com
Wed Aug 6 20:03:30 CEST 2014

hi Ben,

One problem with this comparison is that, without replicates from at
least one site, the statistical methods have no way of assessing the
biological and technical variability of the experiment. Just like with
a t-test, the question, is 2 < 6 depends on how much variability we
expect from sampling again and again. For more information, read the
paragraph "Experiments without replicates..." in ?DESeq.

were the samples from the different sites prepared and sequenced at
the same facility?

as far as technical aspects of using DESeq/edgeR for metagenomics,
Joey McMurdie has comprehensive instructions here:


On Wed, Aug 6, 2014 at 1:42 PM, Pet Chiang <sdpapet at gmail.com> wrote:
>  I am working on my metagenomic data sets.
> I have annotated my metagenome against COG database. I would like to use
> DESeq to look for the overabundant genes in my site.
> Here is the problem, I only have one site (one metagenome). I would like to
> compare this one to different sites (each of these site has no replication
> too)
> the count data set looks like this:
>  function name                my site      site1 (from US)    site 2 (from
> Japan)  site (from Iceland) .....
> COG1                                 2(counts)    6
> 9                         9
> COG2                                 5
> 5                        8                          8
> COG3                                 7
> 9                        8                             0
> .....
> I want to find if any of COG functions in my site is over-representative,
> which means the functional gene counts are overabundant across other sites.
> However, I am not sure  DESeq can do this or not?
> If it can do this, how can I set the groups.
> Best regards,
> Ben
>         [[alternative HTML version deleted]]
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