[BioC] limma example Weaver Data

[Sean Davis]

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 at 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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