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 :
DESEq2
•
reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 9 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
16
replies
2.3k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 4 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
3
votes
1
reply
235
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
i.sudbery
▴ 40
3
votes
3
replies
179
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
WardDeb
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 10 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
705
views
DESeq2 setting significant p-value
DESeq2
updated 8 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
9
replies
281
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
Alexandre
• 0
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 23 days ago by
Michael Love
41k • written 24 days ago by
RL
• 0
1
vote
2
replies
223
views
How to retrieve detailed regression results from deseq2
DESeq2
16 days ago • updated 8 days ago
Weiqian
▴ 10
1
vote
2
replies
381
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
10 days ago • updated 1 day ago
ussarizona
▴ 10
1
vote
1
reply
156
views
DESeq2 - Missing values in count matrix
DESeq2
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Hong Thu
• 0
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 26 days ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
1
vote
4
replies
205
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
3 days ago • updated 1 day ago
winwater0928
• 0
1
vote
3
replies
137
views
Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
122
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 1 day ago by
Michael Love
41k • written 1 day ago by
JalapenoCornbread
• 0
1
vote
2
replies
175
views
Design Matrix within group comparison more than two groups
DESeq2
15 days ago • updated 14 days ago
hemantcnaik
• 0
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
25 days ago • updated 24 days ago
Layal
• 0
0
votes
1
reply
144
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 17 days ago by
Michael Love
41k • written 18 days ago by
Adelaide
• 0
0
votes
1
reply
117
views
covariate with negative and positive values
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
Brynn
• 0
0
votes
4
replies
574
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 11 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
2
replies
148
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
joshua.mannheimer
• 0
0
votes
7
replies
391
views
DESeq filtering specific to contrasts
DESeq2
updated 8 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
0
votes
4
replies
235
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 25 days ago by
Michael Love
41k • written 25 days ago by
Aidan
• 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
25 days ago • updated 24 days ago
michelafrancesconi8
• 0
0
votes
1
reply
146
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 29 days ago by
Michael Love
41k • written 29 days ago by
Mikushi
• 0
0
votes
8
replies
260
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 2 days ago by
swbarnes2
★ 1.3k • written 4 days ago by
Aaliya
• 0
0
votes
1
reply
87
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 2 days ago by
Michael Love
41k • written 3 days ago by
kcarey
• 0
0
votes
2
replies
114
views
PCA plot suggestions
DESeq2
PCAtools
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Aaliya
• 0
0
votes
4
replies
236
views
DEG with low counts
DESeq2
updated 8 days ago by
Michael Love
41k • written 13 days ago by
Rajat
• 0
0
votes
1
reply
121
views
Bioinformatics student
Des
DESeq2
updated 15 days ago by
hemantcnaik
• 0 • written 15 days ago by
Sahar
• 0
0
votes
2
replies
200
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 17 days ago by
Michael Love
41k • written 22 days ago by
nhaus
▴ 30
0
votes
1
reply
124
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 9 days ago by
ATpoint
★ 4.0k • written 10 days ago by
quanah.hudson
• 0
0
votes
4
replies
201
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
10 days ago • updated 7 days ago
lonn
• 0
0
votes
3
replies
177
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 11 days ago by
Michael Love
41k • written 12 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
92
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 9 days ago by
Michael Love
41k • written 9 days ago by
09191919
• 0
0
votes
1
reply
99
views
rlog transformation
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
ishij9717
• 0
0
votes
1
reply
115
views
Deseq2 Rlog transformation
DESeq2
updated 12 days ago by
ATpoint
★ 4.0k • written 13 days ago by
Sahar
• 0
0
votes
2
replies
225
views
Regressing out batch effects
DESeq2
updated 17 days ago by
Michael Love
41k • written 23 days ago by
kys91240
• 0
0
votes
1
reply
161
views
DESeq2 gives an error and R crashes
DESeq2
16 days ago • updated 15 days ago
Shefali
• 0
39 results • Page
1 of 1
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
Awards
• All
Popular Question
to
Leo Lahti
▴ 40
Scholar
to
James W. MacDonald
65k
Popular Question
to
shepherl
3.8k
Scholar
to
Michael Love
41k
Supporter
to
JKim
• 0
Locations
• All
UPF, Barcelona, Spain,
17 minutes ago
United States,
38 minutes ago
The city by the bay,
56 minutes ago
United States,
1 hour ago
France,
1 hour ago
Traffic: 536 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