Hi Dimitra,

Gabe is correct that if you want a report that includes all three coefficients in the same table, you'll have to design a function to select results from each coefficient and make a data.frame from them. Unfortunately, I don't have a quick piece of code to drop in.

Now for your other problem...

> 
> thanks for the fast reply, but although there are three tables
> successfully created in the report, all three contain the exact same
> results, which is the results of the last coefficient.
> I have tried this both on a DESeq2 result including results coming from
> running dds <- DESeq(dds), but also from ddsNoPrior <- DESeq(dds,
> betaPrior=FALSE) and I'm still getting the same behaviour :-/
> Do you have any idea why this is happening? Or do you have some mock
> RNA-seq data where it has worked for you (more than 2 conditions) that I
> could test it on?

This is a bug in ReportingTools. I've fixed this in version 2.3.4, so you'll need to update your version to the latest. In the mean time, you can use the parameter `resultName' instead of `coef' in the publish call, though this is guaranteed to break when you update your version of ReportingTools.

Thanks for finding this, and sorry for the confusion,

Best,

Jason

-- 
Jason A. Hackney, Ph.D.
Bioinformatics and Computational Biology
Genentech, Inc.
hackney.jason@gene.com
650-467-5084


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