[BioC] ANOVA analysis using edgeR

[Ceca Bojic]

I khy

Sent from my iPhone

> On Aug 1, 2014, at 12:52 AM, Yogender Gowtham <ygowtha at g.clemson.edu> wrote:
> 
> Hello All:
> 
> I am Yogender Gowtham, a graduate student from Clemson University. We are
> using RNA-Seq to investigate the transcriptional changes of Chinese Hamster
> Ovary (CHO) cells during serum-free adaptation. Our experiment has two cell
> lines, say Y and Z,  under 3 different serum concentrations, say, 10%, 5%
> and 0%. Cell line Z could not be adapted to 0% serum condition and hence we
> have unbalanced set of conditions. For clarity, the conditions are listed
> below
> 
> A - Y at 0%                 D - Z at 5%
> B - Y at 5%                 E - Z at 10%
> C - Y at 10%
> 
> We have come up with 9 different pairwise comparisons based on the
> scientific questions we want to answer. But performing so many pairwise
> comparisons will lead to more liberal FDR values. Hence we want to perform
> ANOVA analysis on all the five conditions.
> 
> Based on section 3.2.6 which explains how to perform ANOVA-like analysis.
>> From what I understand, it contrasts each column with intercept and will
> list any differences that are non-zero (B-A, C-A, D-A, E-A). But ideally we
> want B-A, B-C, B-D, E-B, C-A, D-C, E-C, D-A, or E-A comparisons in an ANOVA
> test.
> 
> If anyone can suggest a method on edgeR to perform ANOVA tests, that will
> be perfect. If not, can someone suggest other possible packages that could
> help me do an ANOVA analysis on multiple groups.
> 
> Regards
> 
> 
> Yogender Kumar Gowtham
> Graduate Research Assistant
> Clemson University
> Department of Bioengineering
> 202 Biosystems Research Complex
> Clemson, SC
> (864)650-7451
> 
>    [[alternative HTML version deleted]]
> 
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