Hi,

  I had a groups of samples with 12 different conditions. I followed the DESeq2 tutorial in Bioconductor, and then plot the rejections:

{plot(metadata(res)$filterNumRej, 
     type="b", ylab="number of rejections",
     xlab="quantiles of filter")
lines(metadata(res)$lo.fit, col="red")
abline(v=metadata(res)$filterTheta)}

The figure shows that there are a lot of rejections, does this make sense?

https://imgur.com/a/lwtvGOF

```{r}
resNoFilt <- results(dds, independentFiltering=FALSE)
addmargins(table(filtering=(res$padj < .1),
                 noFiltering=(resNoFilt$padj < .1)))
```

         noFiltering
filtering FALSE  TRUE   Sum
    FALSE 19068     0 19068
    TRUE    845 14266 15111
    Sum   19913 14266 34179

Thanks & regards,

Raymond

Take a look at the PCA plot. Also see the section of the vignette on LFC threshold tests.