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emptyDrops
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4
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`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
20 months ago • updated 19 months ago
Peter Hickey
▴ 670
5
votes
1
reply
4.4k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 19 months ago by
Stefano Mangiola
▴ 10 • written 4.6 years ago by
shbrief
▴ 20
4
votes
5
replies
1.9k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils
scRNA-seq
emptyDrops
simplesinglecell
cell calling
updated 3.4 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
C T
▴ 140
0
votes
2
replies
999
views
Scalability of emptyDrops() running times
dropletutils
emptydrops
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
rosano
• 0
0
votes
1
reply
622
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 10 months ago by
Peter Hickey
▴ 670 • written 10 months ago by
sandra.garces.19
• 0
0
votes
2
replies
142
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
10 days ago
rocanja
▴ 60
1
vote
1
reply
1.0k
views
Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils
emptyDrops
10x
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
Peter Hickey
▴ 670
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Gordon Smyth
50k
Regarding your original question, limma results will change if you remove one of the conditions because the residual standard deviations wi…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Thank you for reply early on Saturday morning. Sorry if the question is not clear to you. Here is my code when compare 3 conditions: d…
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The batch effect is not perfectly aligned with sex, with 3 samples not agreeing. I suggest you investigate the two male samples in the top …
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Please make a start on reading the documentation. Perhaps start with Section 1.4 of the [edgeR User's Guide](https://bioconductor.org/packa…
Answer: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Gordon Smyth
50k
I don't know what you mean when you say that you using limma to compare pathway scores from GSVA. Please show your code so we know what you…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Answer: The difference when using Limma compare between 3 conditions vs 2 conditions
A: Removing batch effect with limma::removeBatchEffect() actually exacerbates the e
A: Removing batch effect with limma::removeBatchEffect() actually exacerbates the e
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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