dosage analysis

[evanharrell]

Hi everyone,

I designed an experiment looking at differential expression in a certain group of cells after overexpression of a gene in a neighbouring group of cells. In order to overexpress my gene (and overexpress its control gene in the controls), I needed to use temperature induction (those familiar with the dmel GAL4/GAL80ts system, that is what i used). That leaves me with RNA-seq data of the following description

12 Hr heat induction of expression - 3 bio reps of treatment / 3 bio reps of control

24 Hr heat induction of expression - 3 bio reps of treatment / 3 bio reps of control

48 Hr heat induction of expression - 3 bio reps of treatment / 3 bio reps of control

It seems that DESeq/edgeR only take factors as the variables. Are there any DE platforms that allow gene expression to be modelled against dosage/time?

[dpryan]

DESeq/edgeR will handle that just fine. You can input numeric values into your model if that's what you want (search the bioconductor email list for a number of examples of this being done).

[evanharrell]

I have checked the list, and have not managed to find what you are talking about. I do see many messages where Simon and Wolfgang ask for more details on the experiments (most of these go back to 2012 and 2011), but it seems they direct people away from doing time course analysis. Please send a link to the messages you are talking about.

[evanharrell]

I did find a thread on SEQanswers from June that you helped on. I will try your recommendations from that.