[BioC] Finding genes with similar trend

[Steve Lianoglou]

Hi,

On Tue, Mar 11, 2014 at 9:26 AM, Christian De Santis
<christian.desantis at stir.ac.uk> wrote:
> Dear List,
>
> I have data from a nutritional microarray experiment with 5 treatments where one component of the diet is varying in different proportions.
> I have visually identified some genes that in my opinion share a common and possibly interesting trend. However, I was wondering if it exists a way to model this trend and extract other genes from the list that fit this trend. It is not necessarily a linear increase or decrease of expression (I know how to do that in Limma).
>
> Perhaps anyone is aware of any functions of existing packages that can perform such a task? Thanks very much for your help, as usual!

Are you looking to do something like what the voom folks did in Figure
11 of their paper:

voom: precision weights unlock linear model analysis tools for RNA-seq
read counts
http://genomebiology.com/2014/15/2/R29

This is a direct link to the figure:
http://genomebiology.com/2014/15/2/R29/figure/F11

If so, I reckon reading the paper + methods should give you a good
idea about how to start.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech