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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
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 27 days ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 11 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
706
views
DESeq2 setting significant p-value
DESeq2
updated 8 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
4
replies
576
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
1
vote
2
replies
464
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
10 days ago • updated 1 day ago
ussarizona
▴ 10
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 24 days ago by
Michael Love
41k • written 24 days ago by
RL
• 0
0
votes
7
replies
393
views
DESeq filtering specific to contrasts
DESeq2
updated 8 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
2
votes
9
replies
289
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
Alexandre
• 0
0
votes
8
replies
272
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 3 days ago by
swbarnes2
★ 1.3k • written 4 days ago by
Aaliya
• 0
3
votes
1
reply
245
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
i.sudbery
▴ 40
0
votes
4
replies
237
views
DEG with low counts
DESeq2
updated 9 days ago by
Michael Love
41k • written 13 days ago by
Rajat
• 0
0
votes
4
replies
236
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 25 days ago by
Michael Love
41k • written 26 days ago by
Aidan
• 0
1
vote
2
replies
226
views
How to retrieve detailed regression results from deseq2
DESeq2
17 days ago • updated 8 days ago
Weiqian
▴ 10
0
votes
2
replies
225
views
Regressing out batch effects
DESeq2
updated 18 days ago by
Michael Love
41k • written 23 days ago by
kys91240
• 0
1
vote
4
replies
220
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
4 days ago • updated 2 days ago
winwater0928
• 0
0
votes
4
replies
203
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
10 days ago • updated 8 days ago
lonn
• 0
0
votes
2
replies
202
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 18 days ago by
Michael Love
41k • written 23 days ago by
nhaus
▴ 30
3
votes
3
replies
187
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
WardDeb
• 0
0
votes
3
replies
180
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 11 days ago by
Michael Love
41k • written 12 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
175
views
Design Matrix within group comparison more than two groups
DESeq2
15 days ago
hemantcnaik
• 0
0
votes
1
reply
161
views
DESeq2 gives an error and R crashes
DESeq2
17 days ago • updated 16 days ago
Shefali
• 0
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
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
25 days ago
michelafrancesconi8
• 0
1
vote
3
replies
150
views
Different Shrunk Log2FC according with reference
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
andrebolerbarros
▴ 20
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
1
reply
146
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 18 days ago by
Michael Love
41k • written 18 days ago by
Adelaide
• 0
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
25 days ago
Layal
• 0
1
vote
3
replies
136
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 1 day ago by
Michael Love
41k • written 2 days ago by
JalapenoCornbread
• 0
0
votes
2
replies
126
views
PCA plot suggestions
DESeq2
PCAtools
updated 1 day ago by
Michael Love
41k • written 3 days ago by
Aaliya
• 0
0
votes
1
reply
124
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 10 days ago by
ATpoint
★ 4.0k • written 11 days ago by
quanah.hudson
• 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
1
reply
117
views
covariate with negative and positive values
DESeq2
updated 9 days ago by
Michael Love
41k • written 11 days ago by
Brynn
• 0
0
votes
1
reply
115
views
Deseq2 Rlog transformation
DESeq2
updated 13 days ago by
ATpoint
★ 4.0k • written 14 days ago by
Sahar
• 0
0
votes
1
reply
105
views
rlog transformation
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
ishij9717
• 0
0
votes
1
reply
96
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 3 days ago by
Michael Love
41k • written 3 days ago by
kcarey
• 0
0
votes
1
reply
93
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 9 days ago by
Michael Love
41k • written 10 days ago by
09191919
• 0
38 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)
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James W. MacDonald
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41k
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