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Design Matrix for Limma

So I am trying to make a design matrix for limma. I need to make sure it is a paired analysis because it is time series data. How ever I am not sure I am doing it right. 

filenames <- row.names(pData(rawData))
person <- factor(c((seq(1,13, by=1)),seq(1,14,by=1),seq(1,14,by=1)
                   ,seq(1,14,by=1),Filter(function(x) x != 8 & x != 9, 1:14)))

time <- factor(c( rep.int(1, 13)),rep.int(2,14),rep.int(3,14)
                 ,rep.int(4,14),rep.int(5,12)))

design <- model.matrix(~0 + person + time )
rownames(design)<- filenames

This is the matrix I make. I input into the model and my probelist is super long and does not look right. I want to compare between the 5 times points but at the same time take into account the that they are the same person. Any help?

Thanks.

r limma microarray affymetrix
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updated by Devon Ryan Devon Ryan • written by hakimelakhrass hakimelakhrass

I did do that. My example is based on that section. They only had one example though.

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written by hakimelakhrass hakimelakhrass

Could you edit your definition of time so that it compiles, please:

time <- factor( c( rep.int(1,13), rep.int(2,14), rep.int(3,14),
              rep.int(4,14), rep.int(5,12)))

I was wondering why you are using time as a factor. Rather than trying to perform contrasts at each time point, I'd try and find time-related trends using polynomial regression.

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written by russhh russhh

This appears to be a rendering bug in biostars. Everything renders correctly in the preview but not the final page. I'll play around with things until they render in the final version in a valid manner.

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written by Devon Ryan Devon Ryan

That is just how I saw it being done. To make a contrast matrix and try to see the differences. Do you have any tutorials or R packages in using polynomial regression for this?

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written by hakimelakhrass hakimelakhrass

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