Dear Som,
The usual way to deal with the donor effect is to include a factor for
donor in the design matrix. This ensures that all your comparisons
are
made within donor:
design <- model.matrix(~Donor+Dose*Time)
Usually I would prefer to correct for the batch effect in the design
matrix, rather than pre-correcting with ComBat, because it ensures
that
the degrees of freedom reflect that fact that batch correction the has
been done.
Best wishes
Gordon
> Date: Fri, 22 Apr 2011 13:49:59 -0400
> From: somnath bandyopadhyay <genome1976 at="" hotmail.com="">
> To: <genome1976 at="" hotmail.com="">
> Cc: bioconductor-bounces at r-project.org, bioconductor at
stat.math.ethz.ch
> Subject: [BioC] LIMMA: donor effect
>
>
> I am trying to analyze microarray data for a project where whole
blood
> was collected from 4 different donors and was treated with a
compound at
> 2 time-points at 4 different doses. I am interested in genes that
are
> differentially regulated with dose, with time and also dose*time.
When I
> run a PCA on the entire data, the separation of groups is mainly by
> donors. How do I run a limma analysis (factors, design matrix) to
get to
> the genes of interest (mentioned earlier)? I am not interested in
genes
> that are differentially expressed across donors. Any suggestion
would be
> greatly appreciated.
>
> Thanks,
> Som.
>
> Would it be O.K. to use ComBat to get rid off donor effects by
treating
> each donor as a batch?
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:4}}
Thanks for the suggestion, Gordon. I really appreciate it.
> Date: Sun, 24 Apr 2011 09:37:37 +1000
> From: smyth@wehi.EDU.AU
> To: genome1976@hotmail.com
> CC: bioconductor@r-project.org
> Subject: [BioC] LIMMA: donor effect
>
> Dear Som,
>
> The usual way to deal with the donor effect is to include a factor
for
> donor in the design matrix. This ensures that all your comparisons
are
> made within donor:
>
> design <- model.matrix(~Donor+Dose*Time)
>
> Usually I would prefer to correct for the batch effect in the design
> matrix, rather than pre-correcting with ComBat, because it ensures
that
> the degrees of freedom reflect that fact that batch correction the
has
> been done.
>
> Best wishes
> Gordon
>
> > Date: Fri, 22 Apr 2011 13:49:59 -0400
> > From: somnath bandyopadhyay <genome1976@hotmail.com>
> > To: <genome1976@hotmail.com>
> > Cc: bioconductor-bounces@r-project.org,
bioconductor@stat.math.ethz.ch
> > Subject: [BioC] LIMMA: donor effect
> >
> >
> > I am trying to analyze microarray data for a project where whole
blood
> > was collected from 4 different donors and was treated with a
compound at
> > 2 time-points at 4 different doses. I am interested in genes that
are
> > differentially regulated with dose, with time and also dose*time.
When I
> > run a PCA on the entire data, the separation of groups is mainly
by
> > donors. How do I run a limma analysis (factors, design matrix) to
get to
> > the genes of interest (mentioned earlier)? I am not interested in
genes
> > that are differentially expressed across donors. Any suggestion
would be
> > greatly appreciated.
> >
> > Thanks,
> > Som.
> >
> > Would it be O.K. to use ComBat to get rid off donor effects by
treating
> > each donor as a batch?
>
>
______________________________________________________________________
> The information in this email is confidential and
inte...{{dropped:9}}
