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DESEQ2
•
reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 14 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
19
replies
2.4k
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
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 15 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
735
views
DESeq2 setting significant p-value
DESeq2
updated 13 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
1
vote
2
replies
694
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago
ussarizona
▴ 10
0
votes
4
replies
592
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 16 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
1
vote
4
replies
456
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 1 day ago
JKim
• 0
1
vote
6
replies
419
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 28 days ago by
Michael Love
41k • written 29 days ago by
RL
• 0
0
votes
7
replies
405
views
DESeq filtering specific to contrasts
DESeq2
updated 13 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
2
votes
9
replies
342
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
Alexandre
• 0
0
votes
8
replies
323
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 days ago by
swbarnes2
★ 1.3k • written 9 days ago by
Aaliya
• 0
1
vote
4
replies
301
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago
winwater0928
• 0
3
votes
1
reply
297
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
i.sudbery
▴ 40
0
votes
4
replies
260
views
DEG with low counts
DESeq2
updated 13 days ago by
Michael Love
41k • written 18 days ago by
Rajat
• 0
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
22 days ago • updated 13 days ago
Weiqian
▴ 10
0
votes
2
replies
233
views
Regressing out batch effects
DESeq2
updated 23 days ago by
Michael Love
41k • written 28 days ago by
kys91240
• 0
0
votes
4
replies
229
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
15 days ago • updated 12 days ago
lonn
• 0
0
votes
3
replies
217
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
HAK
• 0
0
votes
2
replies
214
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 22 days ago by
Michael Love
41k • written 27 days ago by
nhaus
▴ 30
3
votes
3
replies
213
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
WardDeb
• 0
1
vote
3
replies
202
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
200
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by
Michael Love
41k • written 17 days ago by
andrebolerbarros
▴ 20
3
votes
3
replies
197
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
1
vote
2
replies
189
views
Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago
hemantcnaik
• 0
1
vote
3
replies
187
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 6 days ago by
Michael Love
41k • written 7 days ago by
JalapenoCornbread
• 0
0
votes
2
replies
182
views
PCA plot suggestions
DESeq2
PCAtools
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
0
votes
1
reply
173
views
DESeq2 gives an error and R crashes
DESeq2
22 days ago • updated 21 days ago
Shefali
• 0
0
votes
2
replies
167
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
4 weeks ago • updated 29 days ago
michelafrancesconi8
• 0
0
votes
2
replies
161
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
160
views
DESeq2 - Missing values in count matrix
DESeq2
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
Hong Thu
• 0
0
votes
1
reply
157
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 23 days ago by
Michael Love
41k • written 23 days ago by
Adelaide
• 0
1
vote
1
reply
150
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago • updated 29 days ago
Layal
• 0
0
votes
1
reply
139
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 days ago by
ATpoint
★ 4.1k • written 15 days ago by
quanah.hudson
• 0
0
votes
1
reply
131
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 8 days ago by
Michael Love
41k • written 8 days ago by
kcarey
• 0
0
votes
1
reply
130
views
Bioinformatics student
Des
DESeq2
updated 20 days ago by
hemantcnaik
• 0 • written 20 days ago by
Sahar
• 0
0
votes
1
reply
128
views
Deseq2 Rlog transformation
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Sahar
• 0
0
votes
1
reply
128
views
covariate with negative and positive values
DESeq2
updated 14 days ago by
Michael Love
41k • written 16 days ago by
Brynn
• 0
0
votes
1
reply
123
views
rlog transformation
DESeq2
updated 14 days ago by
Michael Love
41k • written 14 days ago by
ishij9717
• 0
0
votes
1
reply
106
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 14 days ago by
Michael Love
41k • written 14 days ago by
09191919
• 0
0
votes
1
reply
98
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
angelathuynh5
• 0
0
votes
3
replies
93
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 13 hours ago by
ATpoint
★ 4.1k • written 1 day ago by
james.zhang20
• 0
0
votes
1
reply
86
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
Agung
• 0
0
votes
1
reply
85
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
Dev
• 0
1
vote
1
reply
81
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
marcusn
• 0
0
votes
1
reply
75
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Aurora
• 0
0
votes
2
replies
59
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 1 hour ago
kcarey
• 0
0
votes
3
replies
49
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
3 hours ago • updated 2 hours ago
arfranco
▴ 130
0
votes
2
replies
48
views
DESeq2 v1.35.0
DESeq2
updated 7 hours ago by
Michael Love
41k • written 8 hours ago by
Espresso
• 0
48 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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