[BioC] limma modeling, paired samples and continuous variable

[James W. MacDonald]

Hi Michela,

On 4/15/2014 5:05 AM, michela riba [guest] wrote:
> Hi,
> I'm sorry for re-posting the message, but I cannot find it in the archive
> Thanks a lot for attention
>
>
> Hi,
> I would like to model and retrieve differential expression data
> regarding an experimental design in which different patients (9) have different disease classes (3 disease classes) and a feature represented with a percentage (0, 0.50, 0.75,1).
>      some conditions are replicated 2 or 3 times, regarding the disease condition
> Till now I have done an analysis considering Genotype and Disease in the model (as a paired samples analysis)
>
> design <- model.matrix(~Genotype+Disease)
> or
> design <- model.matrix(~0+Genotype+Disease)
>
> now I would like to model also considering
> a continuous variable , namely r
>
> this way: design <- model.matrix(~Genotype+Disease+r)
>
> to see if differential gene expression between two classes of disease are correlated with the r status
>
> but till now it is not possible to gain results
> Coefficients not estimable: r0,5 r0,75 r1
> Warning message:
> Partial NA coefficients for 15246 probe(s)

This indicates that R is using your 'r' data as factor rather than 
numeric. I assume that is not what you want? If so you need to ensure 
that R thinks that 'r' is a numeric vector.

If you really are trying to treat 'r' as a factor, then note that you 
have either an over-specified model (meaning you are trying to estimate 
more parameters than you have observations), or that three of the 
coefficients for 'r' are linear combinations of existing coefficients 
when you already have genotype and disease in the model.

Best,

Jim


>
> if I model
> design <- model.matrix(~Disease+r)
> it goes well, but  it would not consider the different genotypes
>
> I thank you very much for attention
>
> Thanks a lot
>
> Michela
>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] limma_3.18.13
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099