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Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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This part:
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design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa)
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Thank you Tim, this is a great help in getting me started!
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