10 weeks ago
Robert Castelo
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130
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1
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3 months ago
shepherl
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199
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4 months ago
shepherl
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9 months ago
shepherl
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240
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10 months ago
shepherl
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5
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669
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15 months ago • updated 9 months ago
shepherl
3.4k
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5
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20 months ago
shepherl
3.4k
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1.0k
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2.2 years ago • updated 21 months ago
shepherl
3.4k
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2.3 years ago
shepherl
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2.3 years ago
Vincent J. Carey, Jr.
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4
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701
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updated 2.3 years ago by
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3
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2.4 years ago • updated 2.3 years ago
shepherl
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2
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414
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updated 2.5 years ago by
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2.7 years ago
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2
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414
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updated 2.7 years ago by
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558
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140
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2.9 years ago
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3.1 years ago
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572
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0
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459
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3.2 years ago
shepherl
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2
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835
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3.3 years ago • updated 3.2 years ago
shepherl
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6
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485
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3.4 years ago • updated 3.3 years ago
shepherl
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1.9k
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611
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3.5 years ago • updated 3.4 years ago
shepherl
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5
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789
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3.9 years ago • updated 3.6 years ago
shepherl
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458
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3.6 years ago
jmaanaki
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3
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604
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3.7 years ago
shepherl
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479
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3.7 years ago
shepherl
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756
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780
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updated 4.1 years ago by
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620
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693
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8
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1.5k
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updated 6.6 years ago by
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written 6.7 years ago by
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updated 7.2 years ago by
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Answer: struggling to create a heatmap
by
ATpoint
★
2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
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Michael Love
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The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★
2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★
2.1k
You can take over some of the lines from `results()` to find them easily:
```r
suppressPackageStartupMessages(library(DESeq2))
set.s…
Answer: Which genes are outliers in DESeq2?
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Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
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