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SummarizedExperiment summ

3.7 years ago alexgutteridge ▴ 50

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Answer: Deseq2 paired sample in the design is considered as "batch"? by ATpoint ★ 4.9k

It's the same. The analysis will be run with adjustment for the donor differences. Technically, that's the same as a batch, being an unwant…

Answer: Biological replicates consideration in DESeq2 design formula. by ATpoint ★ 4.9k

You clearly see that the PCA is dominated by the effect of "replicate", that is what people often call "batch effect", so unwanted technica…

Comment: Could we detect difference at pathway level but not significant different at gen by purnell • 0

You are absolutely right, and ChatGPT4's comment is accurate: yes, it's entirely possible to find differentially behaving pathways with GSV…

Comment: Position of the legend object in complexHeatmap by caroline.zanchi ▴ 10

I stay away from Rstudio in general too :) I remember having tried something similar without success. When I do ```r draw(pd, x = unit(0…

Comment: Position of the legend object in complexHeatmap by James W. MacDonald 68k

There is a 'just' argument for `draw` that has as its default 'center'. Getting to the corresponding help page is not intuitive though. If …

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