Making a design matrix when the control has a different number of replicates?
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5.8 years ago

Hello,

How do you go about making a design matrix when the control has 8 replicates and the rest have 9. Is it possible or do I have to throw out the one extra from the rest. Thank you!

limma hugene20st • 914 views
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In most cases you can have 8 replicates vs 9. But what is your goal here ?

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The goal is to find DEGs between the time points. So a pairwise comparison between all time points.

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5.8 years ago

Yes you can:

model.matrix(~0 + Treatments, data = data.frame(Treatments = factor(c(rep("Control", times = 8), rep("Treated", times = 9)))))​
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thanks for that helped!

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if I want to compare cancer v/s normal samples, what is the code for design matrix then? Also, there are different numbers of cancer and normal sample. I have no sample replicates.

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That's a whole different kettle of fish. Depends on your experimental design, if your tumour/normal samples are paired, what type of data you have, etc, etc, etc. The design matrix itself is essentially a description of your experimental design. I think you need to do some more reading, or consult with some bioinformatics support at your institution.

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My samples are not paired. I have no one to consult that's why I am here. If you want then I would like to explain my work.

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Then create a new post if it's a new topic to discuss