Thank you so much, Mike.
Very helpful!

I have one last question.
If you have one uninfected individual sampled during three time points,
would you make use of all three transcriptomes in the uninfected group, or
would you discard two of them, considering they are from the same
individual? What do you think is the best practice?

Sincerely, Elin



On Mon, May 27, 2013 at 9:49 PM, Michael Love
<michaelisaiahlove@gmail.com>wrote:

> hi Elin,
>
> On Mon, May 27, 2013 at 8:50 PM, Elin Videvall <Elin.Videvall@biol.lu.se>wrote:
>
>>
>> (I had to add numbers in front of the treatments because otherwise deseq
>> would only test the first two groups against After_infection, but I was
>> also interested in the results from Peak vs Uninfected.)
>>
>
> As in the vignette, you can instead use the levels argument of the
> factor() function to determine the order of the factor levels:
>
> condition <- factor(condition,
> levels=c("Uninfected","Peak_infection","After_infection"))
>
> And later to change the base level, you can either refactor with a new
> order of levels, or you can use the relevel function to change the
> reference level:
>
> condition <- factor(condition,
> levels=c("Peak_infection","Uninfected","After_infection"))
> - or -
> condition <- relevel(condition, "Peak_infection")
>
>
>
>> then my output is different from the first test between the exact same
>> groups. The baseMean remains exactly the same, but the other columns:
>> log2foldchange, p-value, and FDR is not. Why? I would expect only the
>> log2foldchange to switch symbols, and nothing else.
>
>
>
> The output is different because we have added priors on the non-intercept
> coefficients resulting in shrinkage toward log2 fold changes of 0 for genes
> with low counts and/or high dispersion (as in Figure 1 in the vignette). So
> the reported value is not simply log2 of the ratio of means. If you want to
> avoid this shrinkage of coefficients (though we have seen it to make the
> log2 fold changes more reproducible), you can set the 'betaPrior' argument
> to DESeq() to FALSE.
>
> Mike
>

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