Hi Michael,

Is this a single-channel experiment with 6 arrays and two RNA sources?
If yes, then Section 8.5 of the Users Guide has a good example for
computing the design matrix. Chapter 7 is also useful.

http://bioconductor.org/help/bioc-views/2.8/bioc/html/limma.html

Valerie



On 11/12/2010 05:13 AM, Michael MOZAR wrote:
> Hi
> i try to make an analysis of a microarray with the limma package, i'm new
> and inexperiment in this
> my problem is just before doing the lmFit() i have to make a model.matrix,
> but i don't understant very well the process to do that.
> i describe my experiment :
>
> i have 6 samples, three of theme are biological replicate for each
> conditions :
> without iron      with iron :
> -a                    -d
> -b                    -e
> -c                    -f
>
> and i want to see the expressed genes (over or under) in the second
> conditions, the first are the reference
> how i must write my model.matrix to continue my analysis  please ?
>
> i try this one, but it seems not working :
>
>  design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2)))
>
> this is my sessionInfo :
>
>   
>> sessionInfo()
>>     
> R version 2.11.1 (2010-05-31)
> x86_64-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=fr_FR.utf8       LC_NUMERIC=C
>  [3] LC_TIME=fr_FR.utf8        LC_COLLATE=fr_FR.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=fr_FR.utf8
>  [7] LC_PAPER=fr_FR.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] affy_1.26.1   Biobase_2.8.0 limma_3.4.5
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0         preprocessCore_1.10.0 tools_2.11.1
>   
>>     
>   
>
>
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