Hi Ming,

We recommend using the release version.

But if you continue to use v1.0 you can turn off Cooks based filtering with
the argument to DESeq().

It's a good idea to always read the R help, e.g., typing ?DESeq in your R
session.

Then you can make sure you get the help for the software version you are
actually using. If you check the help page, you should see information on
this argument.

Mike
On Feb 11, 2014 11:31 AM, "Ming Yi" <yi02@hotmail.com> wrote:

>
> Hi, Mike and Steve:
>
> Thx a lot for advice. below is my seesioninfo. my version DESeq2_1.0.19 is
> OK?
>
> > show(sessionInfo());
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
> other attached packages:
> [1] DESeq2_1.0.19           RcppArmadillo_0.4.000.2 Rcpp_0.11.0
> [4] lattice_0.20-24         Biobase_2.22.0          GenomicRanges_1.12.5
> [7] IRanges_1.18.4          BiocGenerics_0.8.0
> loaded via a namespace (and not attached):
>  [1] annotate_1.38.0      AnnotationDbi_1.22.6 DBI_0.2-7
>  [4] genefilter_1.42.0    grid_3.0.1           locfit_1.5-9.1
>  [7] RColorBrewer_1.0-5   RSQLite_0.11.4       splines_3.0.1
> [10] stats4_3.0.1         survival_2.37-7      XML_3.98-1.1
> [13] xtable_1.7-1
> >
>
>  ------------------------------
> From: michaelisaiahlove@gmail.com
> Date: Tue, 11 Feb 2014 11:02:00 -0500
> Subject: Re: [BioC] DESeq2 - input data questions
> To: lianoglou.steve@gene.com
> CC: yi02@hotmail.com; bioconductor@r-project.org
>
>  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
>
>
>

	[[alternative HTML version deleted]]

