[BioC] Finding genes with similar trend

[Christian De Santis]

Thanks Steve,

Had a quick look and it seems like it might be it! I am looking forward to read the paper! Thanks for the suggestion!

Christian

-----Original Message-----
From: mailinglist.honeypot at gmail.com [mailto:mailinglist.honeypot at gmail.com] On Behalf Of Steve Lianoglou
Sent: 11 March 2014 16:38
To: Christian De Santis
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Finding genes with similar trend

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



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