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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
•
0
Hi Michael,
I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
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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…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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Gordon Smyth
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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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Gordon Smyth
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It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024).
In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
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This part:
```
design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa)
colnames(design_intercept) <- c("AltSHP_LA","Al…
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