I am relatively new to R and EdgeR.
In the similar package DEseq, there is the possibility of analyzing a
dataset containing replicates only for one condition, but not for the
other.
In this DEseq case only the condition with replicates is considered to
compute the dispersion.
In the part of the User Guide of EdgeR regarding "working without
duplicates" this is not mentioned.
I am asking if something similar is possible with EdgeR and how I
should proceed.
Thanks,
Teresa
Dear Teresa,
edgeR handles the situation that you describe automatically without
any
need for special action on your behalf. It has always done so, going
back
before DESeq and other similar packages existed.
This situation is not mentioned specifically in the edgeR user's guide
because there is no need for any special consideration. It is just
handled organically by the edgeR approach. You just proceed as for
any
edgeR analysis.
Best wishes
Gordon
> Date: Fri, 12 Apr 2013 18:01:32 -0400
> From: Teresa <t.davoli at="" gmail.com="">
> To: bioconductor at r-project.org
> Subject: [BioC] EdgeR- how to work PARTIALLY without replicates
>
> I am relatively new to R and EdgeR.
> In the similar package DEseq, there is the possibility of analyzing
a dataset containing replicates only for one condition, but not for
the other.
> In this DEseq case only the condition with replicates is considered
to compute the dispersion.
> In the part of the User Guide of EdgeR regarding "working without
duplicates" this is not mentioned.
> I am asking if something similar is possible with EdgeR and how I
should proceed.
> Thanks,
> Teresa
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:4}}
