Dear Gordon and limma users,
I'm struggling to understand the design matrices in
the Weaver Data in the Case Studies section of the
limma User's Guide.
In the single loop design, there are 4 arrays and 4
conditions (from two time points and two genotypes).
I tried using modelMatrix() with the target from the
example and assigning ref='P11WT'. I would like to
check the effect 'TimeWt' which is the late vs. early
for WT. Unfortunately, I have been unable to get
Gordon's result (topTable result).
Can someone show me how to get Gordon's design
matrices (two of them in that example) by using the
function modelMatrix() and probably plus
makeContrasts()?
Thanks in advance!
Sincerely,
Wenbin

I guess that you are using an older version of the software. The
Weaver example was expanded and
simplified last October, and full commands are now given to compute
the design matrix, including
use of modelMatrix() and makeContrasts().
Gordon
------ original message --------
[BioC] limma example Weaver Data
Wenbin Liu wnbnl at yahoo.com
Thu May 26 23:25:09 CEST 2005
Dear Gordon and limma users,
I'm struggling to understand the design matrices in
the Weaver Data in the Case Studies section of the
limma User's Guide.
In the single loop design, there are 4 arrays and 4
conditions (from two time points and two genotypes).
I tried using modelMatrix() with the target from the
example and assigning ref='P11WT'. I would like to
check the effect 'TimeWt' which is the late vs. early
for WT. Unfortunately, I have been unable to get
Gordon's result (topTable result).
Can someone show me how to get Gordon's design
matrices (two of them in that example) by using the
function modelMatrix() and probably plus
makeContrasts()?
Thanks in advance!
Sincerely,
Wenbin

Thanks, Gordon! In the expanded example, you have a
common RNA source, the Pool. What if one doesn't have
a common RNA source, such as when it is a loop design
with more than three arrays like the unexpanded Weaver
data? Can you please show me how to generate the
matrices? Thanks!
Wenbin
--- Gordon K Smyth <smyth@wehi.edu.au> wrote:
> I guess that you are using an older version of the
> software. The Weaver example was expanded and
> simplified last October, and full commands are now
> given to compute the design matrix, including
> use of modelMatrix() and makeContrasts().
>
> Gordon
>
> ------ original message --------
> [BioC] limma example Weaver Data
> Wenbin Liu wnbnl at yahoo.com
> Thu May 26 23:25:09 CEST 2005
>
> Dear Gordon and limma users,
>
> I'm struggling to understand the design matrices in
> the Weaver Data in the Case Studies section of the
> limma User's Guide.
>
> In the single loop design, there are 4 arrays and 4
> conditions (from two time points and two genotypes).
> I tried using modelMatrix() with the target from the
> example and assigning ref='P11WT'. I would like to
> check the effect 'TimeWt' which is the late vs.
> early
> for WT. Unfortunately, I have been unable to get
> Gordon's result (topTable result).
>
> Can someone show me how to get Gordon's design
> matrices (two of them in that example) by using the
> function modelMatrix() and probably plus
> makeContrasts()?
>
> Thanks in advance!
>
> Sincerely,
> Wenbin
>
>
>
>

Wenbin,
I have found this link quite useful for figuring out design matrix for
direct designs:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
cmd=Retrieve&db=PubMed&list_uids=14744830&dopt=Abstract
Sean
On May 31, 2005, at 11:32 AM, Wenbin Liu wrote:
> Thanks, Gordon! In the expanded example, you have a
> common RNA source, the Pool. What if one doesn't have
> a common RNA source, such as when it is a loop design
> with more than three arrays like the unexpanded Weaver
> data? Can you please show me how to generate the
> matrices? Thanks!
>
>
> Wenbin
>
> --- Gordon K Smyth <smyth@wehi.edu.au> wrote:
>
>> I guess that you are using an older version of the
>> software. The Weaver example was expanded and
>> simplified last October, and full commands are now
>> given to compute the design matrix, including
>> use of modelMatrix() and makeContrasts().
>>
>> Gordon
>>
>> ------ original message --------
>> [BioC] limma example Weaver Data
>> Wenbin Liu wnbnl at yahoo.com
>> Thu May 26 23:25:09 CEST 2005
>>
>> Dear Gordon and limma users,
>>
>> I'm struggling to understand the design matrices in
>> the Weaver Data in the Case Studies section of the
>> limma User's Guide.
>>
>> In the single loop design, there are 4 arrays and 4
>> conditions (from two time points and two genotypes).
>> I tried using modelMatrix() with the target from the
>> example and assigning ref='P11WT'. I would like to
>> check the effect 'TimeWt' which is the late vs.
>> early
>> for WT. Unfortunately, I have been unable to get
>> Gordon's result (topTable result).
>>
>> Can someone show me how to get Gordon's design
>> matrices (two of them in that example) by using the
>> function modelMatrix() and probably plus
>> makeContrasts()?
>>
>> Thanks in advance!
>>
>> Sincerely,
>> Wenbin
>>
>>
>>
>>
>
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