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Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
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It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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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…
Comment: CombineArrays for EPIC and EPIC V2
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Kim
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Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
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Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first.
Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
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James W. MacDonald
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See `?results`, in particular the lfcThreshold argument.
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