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DEseq2
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1
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104
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
9 days ago • updated 9 minutes ago
ussarizona
▴ 10
1
vote
3
replies
56
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 1 hour ago by
Michael Love
41k • written 18 hours ago by
JalapenoCornbread
• 0
1
vote
4
replies
175
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 8 hours ago
winwater0928
• 0
2
votes
9
replies
261
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 18 hours ago by
James W. MacDonald
65k • written 1 day ago by
Alexandre
• 0
0
votes
1
reply
67
views
PCA plot suggestions
DESeq2
PCAtools
updated 1 day ago by
JKim
• 0 • written 1 day ago by
Aaliya
• 0
0
votes
8
replies
238
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 1 day ago by
swbarnes2
★ 1.3k • written 2 days ago by
Aaliya
• 0
0
votes
1
reply
79
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 1 day ago by
Michael Love
41k • written 1 day ago by
kcarey
• 0
1
vote
3
replies
106
views
Different Shrunk Log2FC according with reference
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
3
votes
1
reply
218
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
i.sudbery
▴ 40
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 3 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
3
votes
3
replies
172
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
WardDeb
• 0
0
votes
4
replies
199
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
9 days ago • updated 6 days ago
lonn
• 0
1
vote
2
replies
221
views
How to retrieve detailed regression results from deseq2
DESeq2
15 days ago • updated 6 days ago
Weiqian
▴ 10
0
votes
7
replies
389
views
DESeq filtering specific to contrasts
DESeq2
updated 6 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
2
votes
5
replies
700
views
DESeq2 setting significant p-value
DESeq2
updated 7 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
4
replies
231
views
DEG with low counts
DESeq2
updated 7 days ago by
Michael Love
41k • written 11 days ago by
Rajat
• 0
0
votes
1
reply
92
views
rlog transformation
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
ishij9717
• 0
0
votes
1
reply
90
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 7 days ago by
Michael Love
41k • written 8 days ago by
09191919
• 0
0
votes
1
reply
115
views
covariate with negative and positive values
DESeq2
updated 7 days ago by
Michael Love
41k • written 9 days ago by
Brynn
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 8 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
0
votes
1
reply
121
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
quanah.hudson
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 9 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
4
replies
573
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 9 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 10 days ago by
Michael Love
41k • written 11 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
112
views
Deseq2 Rlog transformation
DESeq2
updated 11 days ago by
ATpoint
★ 4.0k • written 12 days ago by
Sahar
• 0
1
vote
2
replies
171
views
Design Matrix within group comparison more than two groups
DESeq2
13 days ago
hemantcnaik
• 0
0
votes
1
reply
119
views
Bioinformatics student
Des
DESeq2
updated 13 days ago by
hemantcnaik
• 0 • written 14 days ago by
Sahar
• 0
0
votes
1
reply
159
views
DESeq2 gives an error and R crashes
DESeq2
15 days ago • updated 14 days ago
Shefali
• 0
0
votes
2
replies
197
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 16 days ago by
Michael Love
41k • written 21 days ago by
nhaus
▴ 30
0
votes
1
reply
143
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 16 days ago by
Michael Love
41k • written 16 days ago by
Adelaide
• 0
0
votes
2
replies
225
views
Regressing out batch effects
DESeq2
updated 16 days ago by
Michael Love
41k • written 21 days ago by
kys91240
• 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 21 days ago by
James W. MacDonald
65k • written 21 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
155
views
DESeq2 - Missing values in count matrix
DESeq2
updated 21 days ago by
James W. MacDonald
65k • written 22 days ago by
Hong Thu
• 0
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 22 days ago by
Michael Love
41k • written 22 days ago by
RL
• 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
24 days ago • updated 23 days ago
michelafrancesconi8
• 0
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
24 days ago • updated 23 days ago
Layal
• 0
0
votes
4
replies
235
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 23 days ago by
Michael Love
41k • written 24 days ago by
Aidan
• 0
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 25 days ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
0
votes
1
reply
144
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 28 days ago by
Michael Love
41k • written 28 days ago by
Mikushi
• 0
1
vote
2
replies
217
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
5 weeks ago • updated 29 days ago
Chanderkant Chaudhary
• 0
40 results • Page
1 of 1
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Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
• 0
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…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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