[BioC] edgeR FC calculation question

[Ryan C. Thompson]

Hi Lana,

The fold change (actually log2 fold change) for a contrast is simply 
the sum/difference of all the coefficients in the contrast as you have 
written it. So if Drug.1h, Drug.0h, Placebo.1h, and Placebo.0h are 4 
coefficients in your model, then your "DrugvsPlacebo.1h" contrast works 
out to:

1 * Drug.1h + -1 * Drug.0h + -1 * Placebo.1h + 1 * Placebo.0h

The logFC for each gene is computed by substituting the fitted values 
for each coefficient into the expression that you specify as the 
contrast.

-Ryan

On Fri 17 Jan 2014 01:08:51 PM PST, Lana Schaffer wrote:
> Hi,
> Can you please tell me how the FC is calculated in the following test in edgeR?
> DrugvsPlacebo.1h = (Drug.1h-Drug.0h)-(Placebo.1h-Placebo.0h),
>
> Lana Schaffer
> The Scripps Research Institute
> Biostatistics, Informatics
> DNA Array Core Facility
> 858-784-2263
>
>
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