[BioC] which one should I choose in DEseq

[Simon Anders]

Dear Liyue

On 03/01/14 04:23, liyue [guest] wrote:
> I have a RNA-seq dataset.
>
> The format is:
>
> gene_id	day0	day2	day6	day9
> mmu-let-7a-5p	3862	456	650	4991
> mmu-let-7b-5p	462	222	97	56
> mmu-let-7c-5p	13081	777	724	1953
> mmu-let-7d-5p	12357	679	729	5017
>
> I just want to find the differentially expressd genes during four days. Which one can I choose in DEseq?
> 3.1 between two experimental conditions
> 3.2 working partially without replicates
> 3.3 working without sny replicates

If you want advice on how to analyze your data, you need to tell us what 
_exactly_ you want to do. What is the experimental design? What is the 
biological question? What do _you_ mean by "differentially expressed 
genes"?

I point this out because there is no one single way to analyse RNA-Seq 
data, especially not when time series are involved.

I'm also bit puzzled by your question. You do not have replicates and 
you have already found out that there is a section "working without any 
replicates". Also, you have _four_ time point, so the section "between 
_two_ experimental conditions" is clearly not applicable.

   Simon