Hello,
I am using EdgeR to analyse RNAseq data.
I would like to know whether I should use several paired analyses or a
blocking analysis for this paired experiment:
I have cells from3 patients. For each patient, I have 3 conditions:
cells were either Non treated, treated with drug 1, or treated with
drug 2.
I would like to know what each drug does, and the difference between
them.
I have a doubt because in this case a block would be one patient, so
cells are exactly the same.
Then I have the same question whether to use several paired analyses,
or first a blocking analysis for each group followed by several paired
analyses, or another kind of analysis for those paired experiments:
cells from 3 healthy patients , either treated or not with a hormone .
cells from 3 patients with disease D1, either treated or not with the
hormone
cells from 3 patients with disease D2, either treated or not with the
hormone.
I would like to know what is wrong in the response to the hormone in
patients with disease D1 and D2.
thank you very much,
anna
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Sent via the guest posting facility at bioconductor.org.
Dear Anna,
> Date: Tue, 23 Oct 2012 01:27:13 -0700 (PDT)
> From: "anna [guest]" <guest at="" bioconductor.org="">
> To: bioconductor at r-project.org, m.nadira at yahoo.fr
> Subject: [BioC] experiment design in EdgeR
>
>
> Hello,
> I am using EdgeR to analyse RNAseq data.
> I would like to know whether I should use several paired analyses or
a blocking analysis for this paired experiment:
> I have cells from3 patients. For each patient, I have 3 conditions:
cells were either Non treated, treated with drug 1, or treated with
drug 2.
> I would like to know what each drug does, and the difference between
them.
> I have a doubt because in this case a block would be one patient, so
cells are exactly the same.
Thsi is a blocked design, described in Section 3.4.2 "Blocking" in the
edgeR User's Guide.
> Then I have the same question whether to use several paired
analyses, or
> first a blocking analysis for each group followed by several paired
> analyses, or another kind of analysis for those paired experiments:
>
> cells from 3 healthy patients , either treated or not with a hormone
.
> cells from 3 patients with disease D1, either treated or not with
the hormone
> cells from 3 patients with disease D2, either treated or not with
the hormone.
Just treat this is six groups, following Section 3.3.31 "Defining each
treatment combination as a group" in the edgeR User's Guide.
If you can't find these sections in your User's Guide, then update the
current Bioconductor release.
Best wishes
Gordon
> I would like to know what is wrong in the response to the hormone in
patients with disease D1 and D2.
>
> thank you very much,
> anna
>
> -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
> [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:4}}
Dear Anna,
I replied to your question below too quickly, and my advice below was
too
simple. For better advice, see the response I made a few minutes ago
to
your later posting regarding the same experiment.
Best wishes
Gordon
On Wed, 24 Oct 2012, Gordon K Smyth wrote:
> Dear Anna,
>
>> Date: Tue, 23 Oct 2012 01:27:13 -0700 (PDT)
>> From: "anna [guest]" <guest at="" bioconductor.org="">
>> To: bioconductor at r-project.org, m.nadira at yahoo.fr
>> Subject: [BioC] experiment design in EdgeR
>>
>>
>> Then I have the same question whether to use several paired
analyses, or
>> first a blocking analysis for each group followed by several paired
>> analyses, or another kind of analysis for those paired experiments:
>>
>> cells from 3 healthy patients , either treated or not with a
hormone .
>> cells from 3 patients with disease D1, either treated or not with
the
>> hormone
>> cells from 3 patients with disease D2, either treated or not with
the
>> hormone.
>
> Just treat this is six groups, following Section 3.3.31 "Defining
each
> treatment combination as a group" in the edgeR User's Guide.
>
> If you can't find these sections in your User's Guide, then update
the
> current Bioconductor release.
>
> Best wishes
> Gordon
>
>> I would like to know what is wrong in the response to the hormone
in
>> patients with disease D1 and D2.
>>
>> thank you very much,
>> anna
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:4}}