updated 7.5 years ago by
Martin Morgan
25k
•
written 7.5 years ago by
Welliton de Souza
▴
70
2
votes
2
replies
2.1k
views
1
vote
1
reply
995
views
updated 6.6 years ago by
Martin Morgan
25k
•
written 6.6 years ago by
victoriaccorey
▴
10
4
votes
2
replies
979
views
updated 6.6 years ago by
Hervé Pagès
16k
•
written 6.6 years ago by
jfiksel
▴
30
3
votes
2
replies
835
views
updated 5.4 years ago by
Valerie Obenchain
★
6.7k
•
written 5.4 years ago by
maltethodberg
▴
140
3
votes
3
replies
802
views
updated 5.6 years ago by
shepherl
3.4k
•
written 5.7 years ago by
m.van_iterson
▴
20
0
votes
0
replies
774
views
3
votes
2
replies
644
views
updated 5.1 years ago by
Martin Morgan
25k
•
written 5.1 years ago by
Qiang
▴
70
2
votes
6
replies
628
views
23 months ago
robmaz77
▴
20
1
vote
2
replies
409
views
updated 3.8 years ago by
Martin Morgan
25k
•
written 3.8 years ago by
Qiang
▴
70
0
votes
0
replies
277
views
Recent ...
Replies
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
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?
by
Michael Love
39k
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…
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
Michael Love
39k
Specifying `controlGenes` means it estimates the size factors over those rows. But size factors when used later as offsets in GLM or when u…
Votes
Awards
• All
Popular Question to
Ryan
•
0
Popular Question to
Guido Hooiveld
★
3.5k
Scholar to
James W. MacDonald
62k
Commentator to
Michael Love
39k
Popular Question to
twtoal
▴
10
Locations
• All
Republic of Ireland, 12 minutes ago
France, 22 minutes ago
The city by the bay, 36 minutes ago
Iran, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
Republic of Ireland, 12 minutes ago
France, 22 minutes ago
The city by the bay, 36 minutes ago
Iran, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
Traffic: 214 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6