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DEseq2
•
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2
votes
5
replies
69
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
4 hours ago • updated 20 minutes ago
Alexandre
• 0
0
votes
1
reply
40
views
PCA plot suggestions
DESeq2
PCAtools
updated 2 hours ago by
JKim
• 0 • written 13 hours ago by
Aaliya
• 0
0
votes
1
reply
72
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 19 hours ago by
Michael Love
41k • written 23 hours ago by
kcarey
• 0
1
vote
3
replies
88
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
0
votes
3
replies
108
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 3 hours ago by
James W. MacDonald
65k • written 1 day ago by
winwater0928
• 0
3
votes
1
reply
186
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
0
votes
8
replies
225
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 11 hours ago by
swbarnes2
★ 1.3k • written 2 days ago by
Aaliya
• 0
3
votes
3
replies
157
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
WardDeb
• 0
0
votes
1
reply
89
views
rlog transformation
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
ishij9717
• 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 0
0
votes
1
reply
97
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
ussarizona
• 0
0
votes
1
reply
113
views
covariate with negative and positive values
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
Brynn
• 0
0
votes
1
reply
116
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 7 days ago by
ATpoint
★ 4.0k • written 8 days ago by
quanah.hudson
• 0
0
votes
4
replies
194
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
8 days ago • updated 5 days ago
lonn
• 0
0
votes
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
220
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 10 days ago by
ATpoint
★ 4.0k • written 11 days ago by
Sahar
• 0
1
vote
2
replies
164
views
Design Matrix within group comparison more than two groups
DESeq2
13 days ago • updated 12 days ago
hemantcnaik
• 0
0
votes
1
reply
118
views
Bioinformatics student
Des
DESeq2
updated 13 days ago by
hemantcnaik
• 0 • written 13 days ago by
Sahar
• 0
0
votes
1
reply
156
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago
Shefali
• 0
0
votes
2
replies
194
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 15 days ago by
Michael Love
41k • written 20 days ago by
nhaus
▴ 30
0
votes
1
reply
141
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 15 days ago by
Michael Love
41k • written 16 days ago by
Adelaide
• 0
0
votes
2
replies
222
views
Regressing out batch effects
DESeq2
updated 15 days ago by
Michael Love
41k • written 21 days ago by
kys91240
• 0
0
votes
2
replies
143
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
153
views
DESeq2 - Missing values in count matrix
DESeq2
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
Hong Thu
• 0
1
vote
6
replies
403
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 21 days ago by
Michael Love
41k • written 22 days ago by
RL
• 0
1
vote
1
reply
138
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
23 days ago • updated 22 days ago
Layal
• 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
23 days ago • updated 22 days ago
michelafrancesconi8
• 0
0
votes
4
replies
232
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by
Michael Love
41k • written 23 days ago by
Aidan
• 0
0
votes
1
reply
142
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by
Michael Love
41k • written 27 days ago by
Mikushi
• 0
2
votes
3
replies
324
views
PCA of different bacterial species
DESeq2
updated 29 days ago by
Michael Love
41k • written 29 days ago by
Laura
▴ 10
1
vote
2
replies
212
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
4 weeks ago • updated 29 days ago
Chanderkant Chaudhary
• 0
0
votes
7
replies
387
views
DESeq filtering specific to contrasts
DESeq2
updated 6 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
4
replies
569
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 8 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 24 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 8 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
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 2 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
696
views
DESeq2 setting significant p-value
DESeq2
updated 6 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 7 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
40 results • Page
1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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