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DESeq2
•
reset
0
votes
0
replies
8
views
LRT, more than two conditions and pairwise comparisons
DESeq2
2 hours ago
boczniak767
▴ 720
0
votes
2
replies
111
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 1 day ago by
Michael Love
42k • written 2 days ago by
shaunpeterson
• 0
0
votes
4
replies
381
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
2 days ago • updated 3 hours ago
Ken C
• 0
4
votes
9
replies
253
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 3 days ago by
ATpoint
★ 4.1k • written 4 days ago by
pangtaihin
• 0
0
votes
3
replies
113
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 4 days ago by
Michael Love
42k • written 5 days ago by
Kasper
• 0
1
vote
2
replies
243
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
5 days ago • updated 3 days ago
BioinfGuru
▴ 30
0
votes
8
replies
502
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 4 days ago by
BioinfGuru
▴ 30 • written 6 days ago by
Eric Katagirya
• 0
0
votes
1
reply
95
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 5 days ago by
Michael Love
42k • written 6 days ago by
piemmea
• 0
0
votes
1
reply
171
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 9 days ago by
ATpoint
★ 4.1k • written 9 days ago by
sajadahmad41454
• 0
0
votes
1
reply
108
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
sajadahmad41454
• 0
2
votes
7
replies
389
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
11 days ago • updated 8 days ago
sajadahmad41454
• 0
2
votes
3
replies
254
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 14 days ago by
ATpoint
★ 4.1k • written 16 days ago by
Reza
• 0
1
vote
1
reply
193
views
Handling multiple differential expression comparisons
DESeq2
updated 14 days ago by
Michael Love
42k • written 16 days ago by
Zainab
▴ 10
0
votes
6
replies
297
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 15 days ago by
swbarnes2
★ 1.4k • written 16 days ago by
arfranco
▴ 130
0
votes
2
replies
166
views
DESeq2 v1.35.0
DESeq2
updated 17 days ago by
Michael Love
42k • written 17 days ago by
Espresso
• 0
0
votes
2
replies
214
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
17 days ago • updated 16 days ago
kcarey
• 0
0
votes
3
replies
225
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 17 days ago by
ATpoint
★ 4.1k • written 17 days ago by
james.zhang20
• 0
1
vote
3
replies
305
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 11 days ago by
ATpoint
★ 4.1k • written 18 days ago by
angelathuynh5
• 0
0
votes
3
replies
302
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 17 days ago by
Michael Love
42k • written 18 days ago by
HAK
• 0
1
vote
1
reply
157
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
marcusn
• 0
0
votes
1
reply
137
views
putting my own expression data in deseq2
DESeq2
updated 19 days ago by
ATpoint
★ 4.1k • written 19 days ago by
Dev
• 0
0
votes
2
replies
170
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
19 days ago • updated 16 days ago
Aurora
• 0
0
votes
1
reply
139
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 19 days ago by
Michael Love
42k • written 20 days ago by
Agung
• 0
3
votes
3
replies
271
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 20 days ago by
ATpoint
★ 4.1k • written 20 days ago by
bioinf
▴ 10
1
vote
3
replies
255
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 23 days ago by
Michael Love
42k • written 24 days ago by
JalapenoCornbread
• 0
2
votes
9
replies
427
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
Alexandre
• 0
0
votes
2
replies
229
views
PCA plot suggestions
DESeq2
PCAtools
updated 23 days ago by
Michael Love
42k • written 24 days ago by
Aaliya
• 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 24 days ago by
Michael Love
42k • written 25 days ago by
kcarey
• 0
1
vote
3
replies
236
views
Different Shrunk Log2FC according with reference
DESeq2
updated 25 days ago by
Michael Love
42k • written 25 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
359
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
25 days ago • updated 23 days ago
winwater0928
• 0
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 25 days ago by
Michael Love
42k • written 26 days ago by
i.sudbery
▴ 40
0
votes
8
replies
387
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 24 days ago by
swbarnes2
★ 1.4k • written 26 days ago by
Aaliya
• 0
3
votes
3
replies
253
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 26 days ago by
Michael Love
42k • written 27 days ago by
WardDeb
• 0
0
votes
1
reply
158
views
rlog transformation
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
0
votes
1
reply
128
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
0
votes
4
replies
269
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 29 days ago
lonn
• 0
1
vote
2
replies
745
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 23 days ago
Patadù
▴ 10
0
votes
1
reply
168
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
3
replies
230
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
andrebolerbarros
▴ 20
0
votes
4
replies
292
views
DEG with low counts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Rajat
• 0
0
votes
1
reply
149
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Sahar
• 0
1
vote
2
replies
213
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago
hemantcnaik
• 0
0
votes
1
reply
153
views
Bioinformatics student
Des
DESeq2
updated 5 weeks ago by
hemantcnaik
• 0 • written 5 weeks ago by
Sahar
• 0
0
votes
1
reply
197
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago
Shefali
• 0
1
vote
2
replies
265
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago
Weiqian
▴ 10
0
votes
1
reply
191
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
Adelaide
• 0
0
votes
2
replies
183
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
joshua.mannheimer
• 0
0
votes
2
replies
248
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 5 weeks ago by
Michael Love
42k • written 6 weeks ago by
nhaus
▴ 30
0
votes
2
replies
267
views
Regressing out batch effects
DESeq2
updated 5 weeks ago by
Michael Love
42k • written 6 weeks ago by
kys91240
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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