[BioC] limma troncated design matrix

[Sean Davis]

Actually, I think will result in the same problem.  What you probably 
want is to use a contrast matrix to get what you need.  All of the 
coefficients are with respect to Unos1.  So you need to make a contrast 
matrix to get effects of interest (if they are different than the 
contrast with unos1).  You can change the factor levels if you want 
some other level as the base group.  In what contrasts are you 
interested?

On Oct 6, 2004, at 8:41 AM, Nolwenn Le Meur wrote:

> Sean,
> Thanks for your answer. So if I understand instead of:
>
> sample	UNOS	Etiology
>  s1		1	CMD
>  s2		1	CAD
>  s3		1B	CMD
>  s4		1B	CAD
>  S5		2	CMD
>  S6		2	CAD
>  ...
>
> I should write:
>
> sample	UNOS1	 UNOS1B  UNOS2	Etiology
>  s1		1	0		0	CMD
>  s2		1	0		0	CAD
>  s3		0	1		0	CMD
>  s4		0	1		0	CAD
>  S5		0	0		1	CMD
>  S6		0	0		1	CAD
>  ...
>
> Nolwenn
> ********************************************
> Nolwenn Le Meur
> INSERM U533
> Faculté de médecine
> 1, rue Gaston Veil
> 44035 Nantes Cedex 1
> France
>
> Tel: (+33)-2-40-41-29-86 (office)
>      (+33)-2-40-41-28-44 (secretary)
> Fax: (+33)-2-40-41-29-50
> mail: nolwenn.lemeur at nantes.inserm.fr
> ********************************************
>
> -----Message d'origine-----
> De : Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Envoyé : mercredi 6 octobre 2004 14:30
> À : Nolwenn Le Meur
> Objet : Re: [BioC] limma troncated design matrix
>
>
> This is correct.  You can't specify columns for every factor level or
> your design matrix will be singular.
>
> Sean
>
> On Oct 6, 2004, at 6:30 AM, Nolwenn Le Meur wrote:
>
>> Hi everyone,
>>
>> I'm trying to test the effect of different medical parameters (fators)
>> on my
>> data with limma but I get a troncated design matrix.
>> I've two factors 'UNOS' and 'Etiology' (with 3 and 2 levels
>> respectively)
>> listed below:
>>
>> Target.txt file looks like:
>> sample	UNOS	Etiology
>> s1		1	CMD
>> s2		1	CAD
>> s3		1B	CMD
>> s4		1B	CAD
>> S5		2	CMD
>> S6		2	CAD
>> ...
>>
>> I reading it as a phenoData file.
>>
>> I would like to know the different effects so I create a design 
>> matrix:
>>
>>> design<-model.matrix(~-1+Etiology*UNOS,data=pData(target))
>>> design
>> EtiologyCAD	EtiologyCMD	UNOS1B UNOS2 EtiologyCAD:UNOS1B
>> EtiologyCAD:UNOS2
>> EtiologyCMD:UNOS1B EtiologyCMD:UNOS2
>>
>> but UNOS1 factor level is missing in the design matrix, Am I doing
>> something
>> wrong ?
>>
>> Thanks,
>>
>> Nolwenn
>>
>>
>> ********************************************
>> Nolwenn Le Meur
>> INSERM U533
>> Faculté de médecine
>> 1, rue Gaston Veil
>> 44035 Nantes Cedex 1
>> France
>>
>> Tel: (+33)-2-40-41-29-86 (office)
>>      (+33)-2-40-41-28-44 (secretary)
>> Fax: (+33)-2-40-41-29-50
>> mail: nolwenn.lemeur at nantes.inserm.fr
>>
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