Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Outliers
•
reset
0
votes
1
reply
613
views
Which samples to remove from analysis based on Cook's distance outliers plot
DESeq2
cooks
outliers
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
Michael
• 0
0
votes
3
replies
968
views
dealing with outliers (deseq2)
maxcooks
outliers
zero
counts
DESeq2
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
andreia
▴ 10
1
vote
2
replies
1.0k
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
2.3 years ago
Bex
• 0
8
votes
2
replies
6.8k
views
handling outliers with DESeq2
RNASeqData
DESeq2
Outliers
3.0 years ago
paty
▴ 60
0
votes
2
replies
727
views
Outliers
outliers
Deseq2
3.0 years ago
nolwenn
• 0
7
votes
8
replies
2.0k
views
Cook's Distance Outliers: None reported in results table and "cooksCutoff" modification has no effect
deseq2
outliers
cooks
cooks distance
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
donnenfieldjonah
• 0
2
votes
3
replies
1.9k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
lefeverde
▴ 10
1
vote
7
replies
1.7k
views
skewed differentially expressed gene results - DESeq2
deseq2
differential gene expression
outliers
updated 5.7 years ago by
Ryan C. Thompson
★ 7.9k • written 5.7 years ago by
CE
▴ 20
0
votes
1
reply
1.4k
views
Deseq2 default Cooks distance threshold
Deseq2
outliers
cookscutoff
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
jaime.alvarez.benayas
• 0
1
vote
2
replies
1.1k
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi
normalization
outliers
dna methylation
densityplot
5.8 years ago
peter.fransquet
• 0
0
votes
1
reply
846
views
Removal of outliers after library size correction, can I save this to my dds object?
deseq2
outliers
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
Moose123
• 0
0
votes
6
replies
1.5k
views
weird behaviour DESeq2 1.18.1
deseq2
outliers
version
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
aec
▴ 90
0
votes
4
replies
1.3k
views
significant genes with DESeq2 plenty of outliers and zero counts
zero counts
deseq2
odd results
outliers
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
aec
▴ 90
0
votes
1
reply
1.2k
views
Handling outliers in Deseq2
outliers
deseq2
logfoldchange
6.3 years ago
lirongrossmann
▴ 80
0
votes
10
replies
17k
views
Differential expression due to extreme outliers in DESeq2
deseq2
outliers
6.4 years ago
paul.alto
▴ 50
1
vote
3
replies
5.1k
views
DESeq2: How to manually perform filtering and outlier detection?
deseq2
filtering
outliers
count outliers
updated 6.7 years ago by
Wolfgang Huber
★ 13k • written 6.7 years ago by
heikki.sarin
▴ 10
0
votes
4
replies
2.3k
views
DESeq2, outlier correction, Combat, NMF
deseq2
combat
outliers
NMF
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
noname
• 0
1
vote
1
reply
1.3k
views
Outliers - to remove or to not remove that is the question
outliers
rna
microarray
updated 6.9 years ago by
chris86
▴ 420 • written 6.9 years ago by
bhgyu
▴ 30
1
vote
8
replies
3.1k
views
[DESeq2] Automatic outlier detection and replacement with continuous variables
deseq2
outliers
RNAseq
differential gene expression
7.1 years ago
cajawe
• 0
0
votes
9
replies
1.7k
views
DESeq2 influence of 2 samples
deseq2
outliers
differential gene expression
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
gregory.l.stone
▴ 10
0
votes
7
replies
3.6k
views
Deciding on cooks cutoff value DESeq2
deseq2
differential gene expression
outliers
bioconductor
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
gregory.l.stone
▴ 10
0
votes
3
replies
1.0k
views
DESeq outlier detection for unbalanced groups
deseq2
deseq
outliers
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
akaever
▴ 30
3
votes
3
replies
1.6k
views
How to define an outlier array from PCA?
microarray
PCA
outliers
sample outliers
limma
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
serpalma.v
▴ 60
8
votes
17
replies
14k
views
WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA
Sample Size
Outliers
updated 8.6 years ago by
mh.manoj
• 0 • written 9.2 years ago by
brohawndg
▴ 150
0
votes
0
replies
2.2k
views
Modeling count data that is zero inflated with negative binomial hurdle regression
pscl
outliers
updated 9.1 years ago by
Sean Davis
21k • written 9.1 years ago by
mrk.carty
▴ 30
25 results • Page
1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Awards
• All
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Popular Question
to
Bine
▴ 40
Locations
• All
France,
just now
United Kingdom,
just now
France,
7 minutes ago
UPF, Barcelona, Spain,
17 minutes ago
Germany,
19 minutes ago
Traffic: 871 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6