Simon Anders | 24 Dec 15:10 2013
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Re: DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments

On 24/12/13 15:08, Simon Anders wrote:
> For the interaction, you get not only a p value but also a log2 fold
> change in the results data frame. The latter is an estimate of the log2
> of the double ratio you mention. Using this estimate is preferrable to
> simply using the ratio itself because it has undergone empirical-Bayes
> shrinkage, which gets rid of the exaggerated values that the naive ratio
> tends to exhibit when counts are low.

Just noticed that you were using DESeq1, not DESeq2. Shrinkage is 
offered only in DESeq2 (and it might be useful for you to switch for 
this reason). In DESeq1, the reported log fold change is the unshrunken 
GLM estimate, which, in case of a balanced design, tends to be pretty 
close to the actual log ratio.

   Simon

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