Hi Rob,
On Aug 1, 2014 2:20 PM, "rob yang" <nextgame@hotmail.com> wrote:
>
> Hello DESeq community,
>
> I wanted to ask how basemean and log2foldchange are calculated.
>
> 1) From mcol(mcol(dds_fit)), the basemean is denoted as "basemean over
all rows". But I can't pin down what "all rows" this means. For a single
transcript, my manual mean calculation of all counts across all replicates,
all conditions do not equal to the DESeq reported basemean for a single
transcript.
>

Yes that is kind of funny, I should change it to say "columns" or
"samples". It is just as Steve described, the mean of normalized counts for
all samples in the dds.

> 2) log2foldchange seems to be changing with the contrasting variable.
This is a little surprising since I'd expect log2foldchange to be a static
number when comparing two conditions, and the contrasting variables only
dictate testing for significance, ie., p-value.
>

I don't follow. Can you say more what you mean by changing with contrasting
variable

Mike

> Thank you in advance.
>
> -Rob
>
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