DESeq2 alpha filter not working
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Entering edit mode
Chris • 0
@chris-9148
Last seen 8.4 years ago
United Kingdom

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?

 

deseq2 • 1.3k views
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@mikelove
Last seen 4 hours ago
United States
Upgrade to the latest version of Bioc and DESeq2 (v1.10) and summary() will automatically use the alpha from results() Or use the alpha argument of summary()
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Entering edit mode

Ah, I didn't see summary needs the alpha filter as well.

Thanks for the quick response.

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