Design matrix for missing group
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ijvechetti • 0
Last seen 11 months ago
United States

Hello all,

I have an array with 8 groups and 4-time points (3 replicates in each), with the exception of 1 timepoint where the rats died. Reading about this missing group on Limma guideline, I think the best strategy would be the group-mean parametrization strategy?

Imaging I have groups (1,2,3,4,5,6,7 and 8) and time points (1mo, 3mo, 6mo, 12mo), how could I determine the changes over time doing the parametrization strategy, assuming I'm correct on that one.

Thanks in advance

limma • 295 views
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Last seen 8 hours ago
WEHI, Melbourne, Australia

I generally recommend the group-means design matrix setup because of its simplicity and ease of interpretation. Whether there is a missing group or not makes no difference -- the approach is the same.

Entering edit mode

Thanks Gordon, for your quick answer. Coming back to my design, how could I determine changes over time doing this strategy?

Sample 1 is my control.

I did the contrasts for each month: Cont <- makeContrasts("2-1", "3-1", .......... levels=design)

Now I would like to determine if there is any change over time, but I'm not sure how to make the appropriate design. Would be something like that?

Cont.group2 <- makeContrasts((2-1)-(3-1)-(6-1)-(12-1), levels=design)

Thanks once again


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