[BioC] DESeq - working with more than 2 conditions

[Simon Anders]

On 16/01/13 05:18, Shanrong Zhao wrote:
>
> Section 4 in DESeq tutorial covers multiple-factor, but multi-factor is NOT
> equal to multiple conditions.
>
> I believe in real world, more often you have more conditions than just two.
> Let's say I have a study:
> 1. 3 conditions: control, treat_1, and treat_2
> 2. Triplicates in each condition
> 3. comparisons:
>      a:  treat_1 vs control
>      b:  treat_2 vs control
>
> Questions: how to do it using DESeq?  I did google around, search
> Seqanswrs ..., but still wondering.

If you do not have any factors beyond your more-than-two conditions, you 
simply call nbinomTest for each comparison, always giving the two 
conditions you want to compare as second and third argument.

   Simon