Hi,

I'm trying out DESeq2 (v1.8.2, R 3.2.2) for the first time and following the std bioconductor documentation, but am finding that the results() function is ignoring the 'alpha' parameter e.g.

>dds <- DESeqDataSetFromMatrix(countData = geneCounts, colData = DataFrame(groups), design = ~ V2)
>dds <- DESeq(dds)
>res <- results(dds)
>res05 <- results(dds, alpha=0.05)
>summary(res)
out of 6956 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up)     : 1594, 23%
LFC < 0 (down)   : 1592, 23%
outliers [1]     : 0, 0%
low counts [2]   : 348, 5%
(mean count < 1.1)

>summary(res05)
out of 6956 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up)     : 1594, 23%
LFC < 0 (down)   : 1592, 23%
outliers [1]     : 0, 0%
low counts [2]   : 348, 5%
(mean count < 1.1)

What's the problem here?