Hi Noa,

Thanks for reporting in. ​This sounds like the same problem that a user had
in November:

http://permalink.gmane.org/gmane.science.biology.informatics.conductor/51749
​

​If you are using the updated release version (>= 1.2.6), there should have
been a warning printed when you build the DESeqDataSet that you should set
betaPrior=FALSE because factors are present in the design with 3 or more
levels.

In the devel branch of DESeq2 (v1.3), we have implemented a solution that
allows using a prior on log fold changes for factors with 3 or more levels
results. Then DESeq() or nbinomWaldTest() will provide symmetric results
regardless of the base level and it takes care of this situation with
nonzero log fold changes from contrasts in which both conditions have zeros.

With future questions please
 post your full code, the output of sessionInfo()
​, as this helps us provide better answers.​

Mike
On Jan 7, 2014 8:49 AM, "Noa Henig" <ntzunz@gmail.com> wrote:

> Hi,
> I am using DESeq2 to get differential expression of 45 samples which
> represent 26 different conditions.
> I read that the calculation of the fold change in changed DESeq2 and
> affects the genes having low counts more than the highly expressed genes.
> However, I found genes that had zero counts in series of  4 samples (2
> replicates in each of 2 conditions), while their log2fold change was 3.
> what is the reason for that? or how can this be prevented?
>
> I used the nbinomWaldTest and did not replace outliers with the trimmed
> mean since I have only 2 replicates per condition.
>
> I'd appreciate your help very much,
> Noa Henig
>
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