Yes, Steve is on it. I assumed you were using the current release version
of Bioconductor (2.13) with DESeq2 v1.2.

In v1.0, the cooksCutoff argument was in DESeq().


> Also from your experience, if Cook's filtering is taken out, validation
> rate much worse? In reality, some genes might have large variation than
> others such as cancer-related genes. What do you think?


​Cook's filtering is just a heuristic, so it's hard to give general advice.
The point is to help identify cases when individual samples have too much
influence on the log fold changes. I would recommend plotting the counts of
genes with large Cook's distance:

# get the genes with highest max(Cook's distance for each sample)
cooks <- mcols(dds)$maxCooks
idx <- order(-cooks)
# plot the normalized counts for the top gene by max Cook's distance
plot( counts(dds,normalized=TRUE)[ idx[1], ], main=paste("Max Cook's:",
cooks[idx[1]]) )

You can decide for yourself where to set the filter by setting cooksCutoff
= x.

Note that large variance alone will not lead to filtering; the filtering
comes in when the variance for a majority of samples is small, but a
minority of samples have extreme counts which have large influence on the
log fold changes.

For your experiment, if the subject variable is explaining a lot of the
variance I would make sure to include it in the design, to help isolate the
true condition effect.

Mike


On Tue, Feb 11, 2014 at 10:38 AM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi,
>
> On Tue, Feb 11, 2014 at 7:11 AM, Ming Yi <yi02@hotmail.com> wrote:
> > Hi, Mike:
> >
> >
> >
> > Thanks a lot for the prompt response and input, which is very helpful
> >
> > Since some of the genes seem a bit interesting to us, and of course we
> love to keep.
> >
> > However, when I try:
> >
> >> resType <- results(dds, "Type_Tumor_vs_Normal",cooksCutoff=FALSE);
> > Error in results(dds, "Type_Tumor_vs_Normal", cooksCutoff = FALSE) :
> >   unused argument (cooksCutoff = FALSE)
>
> What version of DESeq2 are you using?
> Is the `cooksCutoff` not defined in the documentation when you
> fire`?results` ?
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>

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