Entering edit mode

glennli
•
0

@636e91b3
Last seen 7 weeks ago

Hi, Is it possible to obtain single-sided P-values when using DESeq2 to test ratios of ratios using the likelihood ratio test (ie for Ribosome profiling)? Is it valid to perform a Wald test using the log2FoldChange of the ratio of ratios (output from the LRT mode) from as the contrast, or is this flawed/statistically invalid?

```
dds <- DESeqDataSetFromMatrix(countData = as.matrix(count), colData = as.matrix(coldata),
design= ~ assay + condition + assay:condition)
dds <- DESeq(dds, test="LRT", reduced= ~ assay + condition)
wald <- DESeq(dds)
wald_results <- results(wald, contrast = list("assayrpf.conditionplus"), lfcThreshold = 0, altHypothesis = "greater")
```

Thanks for your help.

Thanks for your reply Mike. Is the Wald test appropriate when testing ratios of ratios? What do I lose from applying this test as compared to the LRT?

It's appropriate yes. By the way you can just do

`results(dds, name="...")`

if you are pulling out one coefficient.I think the LRT is sometimes more robust when there are scattering of 0's and some very large values, so you could always filter such that at least X number of samples have a moderate count.