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DESeq2
•
reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 16 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
19
replies
2.5k
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
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 17 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
744
views
DESeq2 setting significant p-value
DESeq2
updated 15 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
1
vote
2
replies
709
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
17 days ago • updated 8 days ago
ussarizona
▴ 10
0
votes
4
replies
601
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 18 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
1
vote
4
replies
475
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 3 days ago
JKim
• 0
0
votes
7
replies
421
views
DESeq filtering specific to contrasts
DESeq2
updated 15 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
2
votes
9
replies
380
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
Alexandre
• 0
0
votes
8
replies
341
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 10 days ago by
swbarnes2
★ 1.3k • written 11 days ago by
Aaliya
• 0
1
vote
4
replies
315
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
10 days ago • updated 9 days ago
winwater0928
• 0
3
votes
1
reply
308
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 11 days ago by
Michael Love
41k • written 11 days ago by
i.sudbery
▴ 40
0
votes
4
replies
263
views
DEG with low counts
DESeq2
updated 15 days ago by
Michael Love
41k • written 20 days ago by
Rajat
• 0
0
votes
2
replies
245
views
Regressing out batch effects
DESeq2
updated 25 days ago by
Michael Love
41k • written 4 weeks ago by
kys91240
• 0
1
vote
2
replies
240
views
How to retrieve detailed regression results from deseq2
DESeq2
24 days ago • updated 15 days ago
Weiqian
▴ 10
0
votes
3
replies
237
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
HAK
• 0
0
votes
4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
17 days ago • updated 15 days ago
lonn
• 0
3
votes
3
replies
222
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 11 days ago by
Michael Love
41k • written 12 days ago by
WardDeb
• 0
0
votes
2
replies
219
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 25 days ago by
Michael Love
41k • written 29 days ago by
nhaus
▴ 30
3
votes
3
replies
218
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 5 days ago by
ATpoint
★ 4.1k • written 6 days ago by
bioinf
▴ 10
1
vote
3
replies
211
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 8 days ago by
Michael Love
41k • written 9 days ago by
JalapenoCornbread
• 0
1
vote
3
replies
207
views
Different Shrunk Log2FC according with reference
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
204
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 18 days ago by
Michael Love
41k • written 19 days ago by
andrebolerbarros
▴ 20
0
votes
2
replies
201
views
PCA plot suggestions
DESeq2
PCAtools
updated 8 days ago by
Michael Love
41k • written 10 days ago by
Aaliya
• 0
1
vote
2
replies
193
views
Design Matrix within group comparison more than two groups
DESeq2
22 days ago • updated 21 days ago
hemantcnaik
• 0
0
votes
1
reply
174
views
DESeq2 gives an error and R crashes
DESeq2
24 days ago • updated 23 days ago
Shefali
• 0
0
votes
6
replies
172
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 1 day ago by
swbarnes2
★ 1.3k • written 2 days ago by
arfranco
▴ 130
0
votes
2
replies
167
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
joshua.mannheimer
• 0
0
votes
1
reply
161
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 25 days ago by
Michael Love
41k • written 25 days ago by
Adelaide
• 0
0
votes
1
reply
149
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 10 days ago by
Michael Love
41k • written 10 days ago by
kcarey
• 0
0
votes
1
reply
147
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
quanah.hudson
• 0
0
votes
1
reply
135
views
rlog transformation
DESeq2
updated 16 days ago by
Michael Love
41k • written 16 days ago by
ishij9717
• 0
0
votes
1
reply
133
views
covariate with negative and positive values
DESeq2
updated 16 days ago by
Michael Love
41k • written 18 days ago by
Brynn
• 0
0
votes
1
reply
132
views
Bioinformatics student
Des
DESeq2
updated 22 days ago by
hemantcnaik
• 0 • written 22 days ago by
Sahar
• 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 19 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Sahar
• 0
0
votes
1
reply
126
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
angelathuynh5
• 0
0
votes
3
replies
118
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
james.zhang20
• 0
2
votes
2
replies
118
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Reza
• 0
0
votes
2
replies
117
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
3 days ago • updated 2 days ago
kcarey
• 0
0
votes
2
replies
113
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
4 days ago • updated 1 day ago
Aurora
• 0
0
votes
1
reply
111
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 16 days ago by
Michael Love
41k • written 16 days ago by
09191919
• 0
1
vote
1
reply
99
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
marcusn
• 0
0
votes
1
reply
98
views
putting my own expression data in deseq2
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
Dev
• 0
0
votes
1
reply
97
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
Agung
• 0
0
votes
2
replies
82
views
DESeq2 v1.35.0
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Espresso
• 0
0
votes
0
replies
41
views
Handling multiple differential expression comparisons
DESeq2
1 day ago
Zainab
• 0
46 results • Page
1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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