[BioC] Question about median of replicates

[Steve Lianoglou]

Hi,

On Wed, Jul 30, 2014 at 3:44 PM, Sandra Fernandez Moya
<dedeusan at hotmail.com> wrote:
> Hello, I have a very important question, cause we are going to submit a paper in a few hours and now we realize that maybe we have an error, so I want to check with experts beforehand. The thing is I used EdgeR for comparison of 2 groups, Control and Group1, and 3 samples, Control:1 and Group1:2; I followed the basic protocol, because I dont know so much about this analyses and I get a final logFC, that it makes sense and also we checked in the lab. But, now, the referees asked if the logFC was from the data Group1 normalized and with the mean of both and we realize that it was not the mean but seems to be the summ of the counts from each sample of Group1 the ones that the software take for the analysis.

I don't follow what you are saying here.

> Maybe I did something wrong, but can you confirm me this? It shouldnt be, but does EdgeR summ the counts of each replicate and uses it for the analysis?Thanks a lot, and I wait for the answer!Sandra

We can't say much without looking at your code and data.

In edgeR you construct a DGEList to hold your data and perform analysis over.

Let's say this DGEList is called `dlist` in your code, what is the output of:

R> dlist$samples

So we know what your experimental design looks like.

Then please provide all the code you used to do the analysis, and
finally the output of `sessionInfo()`

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech