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Recent Replies
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
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Guille
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Thank you for your answer!
The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
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They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq
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dsull
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https://maayanlab.cloud/clustergrammer/
It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
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Gordon Smyth
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There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler.
I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
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Gordon Smyth
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The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1.
Have you exam…
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Gordon Smyth
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There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
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J
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Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
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J
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Thank you Pierre! I'll try this out with my full data set.
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I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
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I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
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Please include a link when you are recommending a tool. There can be programs with similar names.
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Simple:
```r
data <- lapply(files, read_tsv)
data <- Reduce(merge, data) # or Reduce(full_join, data)
```
<a href="" title="Text added bec…
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