Hello Biocconductor community,

I have been wondering this for some time (and I think I can finally articulate it, somewhat, well enough to have an idea of what to ask)

*How would I interpret DESeq2's padj after setting lfcThreshold and the log2FC is greater than lfcThreshold?*

**An example:**

So if the `results()`

I use within DESeq2 looks like this:

```
res <- results(dds,
contrast=c("Group", second_compar, first_compar),
independentFiltering=TRUE,
alpha=0.05,
pAdjustMethod="BH",
lfcThreshold=1,
altHypothesis="greaterAbs")
```

This would mean:

```
Fold Change = (second_compar/first_compar)
```

so:

```
log2(FC) = log2(second_compar/first_compar)
```

Then, as above, if I set the `lfcThreshold=1`

(so an `FC`

equal to `2`

in `log2(FC)=`

... so `lfcThreshold=1`

would mean the cut-off I am setting is `log2(2)=1`

) and then an `alpha=0.05`

. This means that the `padj`

value for a given `differentially expressed & significant gene`

as defined by a `log2(2) =1`

and an `alpha=0.05`

.

**For everything above, I am somewhat okay in my understanding...**

**Ambiguous territory:**

This is where it gets into "ambiguous territory" for me. Could someone help clear my understanding of what happens when with the "cut-offs" set above, if `Gene X`

that has for example a `log2(10) = 3.321928`

but I am using the cut-off of `log2(2)=1`

and `alpha=0.05`

?

And then to bring it to the actual example above, for hopefully the sake of simplicity, if `first_compar`

in the `Fold Change`

above had a value of `1`

and `second_compar`

had a value of `10`

, so that `log2(FC) = log2(second_compar/first_compar) = log2(10/1) = log2(10) = 3.321928`

and then let me just give a `padj=0.001`

for this `Gene X`

comparison.

If you're still with me after reading all that. Thank you : ) Pratik