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Comment: RNA-seq: samples form different experiments, how to do DGEs?
by
Gordon Smyth
51k
Sorry, I do not understand at all why you are equating batches with labs, since your original question seems to indicate that there are onl…
Answer: GSVA ssGSEA vs. Broad implementation of ssGSEA
by
Tyler Sagendorf
▴ 10
The ssGSEA2.0 code permutes the sorted vector of values in order to calculate permutation ES, rather than permuting the gene labels. See li…
Answer: Its possible to remove annotation names using anno_simple in ComplexHeatmap
by
Tyler Sagendorf
▴ 10
Setting `show_annotation_name=FALSE` in `HeatmapAnnotation()` also works, assuming this is what you were asking for. However, I also agree …
Comment: DESeq2 with unbalanced experimental design
by
Satoshi
• 0
Hey Mike, thanks for the response. We also had a similar issue with 4 vs 8 samples across two conditions. This is single-cell data and I am…
Comment: RNA-seq: samples form different experiments, how to do DGEs?
by
Philippine
• 0
You mean: ![Metadata table with batches ][1] is that correct? Thanks :D [1]: /media/images/b7cca11b-edb1-41b1-9a1e-ea0a13b1
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Answer: DataFrame Character Truncation
Answer: Is there a way to allow elements with no IRanges when subsetting an IRangesList
Answer: Samples used for network inference in RegEnrich
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