Entering edit mode
Dear Steve,
The genes that contribute most to the roast result are the same genes
that
are ranked at the top in a standard genewise DE analysis, i.e., ranked
by
topTable(). Roast doesn't output the leading-edge genes because they
are
already available from the standard genewise analysis.
The z-score is computed from the moderated t-statistics using
zscoreT().
The roast help page says that the cutoff for PropDown and PropUp is z
<
-sqrt(2) and z > sqrt(2). The probability of this is:
> 2*pnorm(-sqrt(2))
[1] 0.1572992
So the genes that contribute to PropUp and PropDown are those that
have
p-value less than 0.1572992 a standard genewise DE analysis.
There is no exact equivalent for romer, but obviously looking at the
genewise DE results will still reveal the most important genes.
Best wishes
Gordon
> Stephen Hoang stephen.a.hoang at gmail.com
> Fri Jan 31 21:58:26 CET 2014
>
> Hi All,
>
> Is there a way to identify the genes that contribute to the gene set
> enrichments calculated by roast/romer? I realize that all of the
genes
> in a given set are contributing to the p-value calculation, but is
there
> a way to get at, for example, the genes that contribute to the
"PropUp"
> value in the output of roast? And is the analogous gene set knowable
in
> the case of romer? I see in roast help page that the "up" and "down"
> genes are categorized as such based on a z-score threshold, but what
are
> the values in this distribution -- global fold changes, fold changes
> within a gene set, or something else altogether?
>
> Thanks in advance,
>
> Steve
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