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Deseq2
•
reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 6 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day 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 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 7 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
694
views
DESeq2 setting significant p-value
DESeq2
updated 5 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
4
replies
564
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
0
votes
7
replies
406
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago
fr8712ca-s
• 0
1
vote
6
replies
401
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 20 days ago by
Michael Love
41k • written 21 days ago by
RL
• 0
0
votes
7
replies
384
views
DESeq filtering specific to contrasts
DESeq2
updated 5 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
2
votes
3
replies
324
views
PCA of different bacterial species
DESeq2
updated 28 days ago by
Michael Love
41k • written 29 days ago by
Laura
▴ 10
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 5 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
0
votes
4
replies
229
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
2
replies
219
views
Regressing out batch effects
DESeq2
updated 15 days ago by
Michael Love
41k • written 20 days ago by
kys91240
• 0
1
vote
2
replies
217
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
1
vote
2
replies
211
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
4 weeks ago • updated 28 days ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
192
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 14 days ago by
Michael Love
41k • written 19 days ago by
nhaus
▴ 30
0
votes
4
replies
191
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 days ago • updated 4 days ago
lonn
• 0
0
votes
3
replies
173
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
12 days ago • updated 11 days ago
hemantcnaik
• 0
0
votes
1
reply
157
views
collapseReplicates dimension error
DESeq2
Dese
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Léa
• 0
0
votes
1
reply
154
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago
Shefali
• 0
2
votes
1
reply
152
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 22 hours ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
1
vote
1
reply
152
views
DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
Hong Thu
• 0
0
votes
2
replies
150
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
22 days ago • updated 21 days ago
michelafrancesconi8
• 0
3
votes
3
replies
145
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
0
votes
2
replies
142
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
joshua.mannheimer
• 0
0
votes
1
reply
141
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
0
votes
1
reply
137
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 15 days ago by
Michael Love
41k • written 15 days ago by
Adelaide
• 0
1
vote
1
reply
135
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago • updated 21 days ago
Layal
• 0
0
votes
4
replies
119
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 6 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
0
votes
1
reply
117
views
Bioinformatics student
Des
DESeq2
updated 12 days ago by
hemantcnaik
• 0 • written 12 days ago by
Sahar
• 0
0
votes
1
reply
112
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 6 days ago by
ATpoint
★ 4.0k • written 7 days ago by
quanah.hudson
• 0
0
votes
1
reply
110
views
covariate with negative and positive values
DESeq2
updated 6 days ago by
Michael Love
41k • written 8 days ago by
Brynn
• 0
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 9 days ago by
ATpoint
★ 4.0k • written 10 days ago by
Sahar
• 0
0
votes
1
reply
95
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ussarizona
• 0
0
votes
1
reply
87
views
rlog transformation
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
ishij9717
• 0
0
votes
1
reply
85
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 6 days ago by
09191919
• 0
1
vote
3
replies
74
views
Different Shrunk Log2FC according with reference
DESeq2
updated 11 hours ago by
Michael Love
41k • written 15 hours ago by
andrebolerbarros
▴ 20
0
votes
1
reply
57
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 7 hours ago by
swbarnes2
★ 1.3k • written 16 hours ago by
winwater0928
• 0
0
votes
1
reply
46
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 3 hours ago by
Michael Love
41k • written 6 hours ago by
kcarey
• 0
40 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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