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DeSeq2
•
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0
votes
1
reply
1.0k
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 16 months ago by
Michael Love
43k • written 17 months ago by
Ειρήνη
• 0
0
votes
1
reply
638
views
unreal negative log2fc values
DESeq2
des
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Atul K.
• 0
0
votes
1
reply
557
views
LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 17 months ago by
Michael Love
43k • written 17 months ago by
K
• 0
1
vote
8
replies
1.9k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Alec
• 0
1
vote
2
replies
3.2k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
17 months ago
sropri
• 0
0
votes
1
reply
566
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Neha
• 0
1
vote
1
reply
771
views
DESeq2 - vst() - log2FC - no replicates
DESeq2
log2FC
vst()
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
lifeonmars
• 0
1
vote
5
replies
1.1k
views
DESeq2 ML Query
DESeq2
updated 16 months ago by
Michael Love
43k • written 17 months ago by
chris2.a.white
• 0
1
vote
3
replies
1.0k
views
Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression
DESeq2
17 months ago • updated 16 months ago
David W. H.
• 0
0
votes
1
reply
722
views
Significant genes in DESeq2 analysis
DESeq2
RNASeq
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
cbio
• 0
1
vote
3
replies
1.9k
views
Combining two bulk RNA seq datasets
RNASeqData
DESeq2
Normalization
17 months ago
Tanvi
• 0
0
votes
1
reply
1.3k
views
In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
DESeq2
updated 17 months ago by
Michael Love
43k • written 18 months ago by
prabath_meemaduma
• 0
2
votes
1
reply
678
views
Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 17 months ago by
Michael Love
43k • written 18 months ago by
hx
▴ 10
2
votes
1
reply
820
views
DESeq2 returns results for group with just one replicate
DESeq2
DifferentialExpression
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
nhaus
▴ 70
1
vote
9
replies
3.2k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
adrip
▴ 10
1
vote
3
replies
1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Ben
▴ 50
3
votes
6
replies
3.5k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 17 months ago by
ATpoint
★ 5.0k • written 2.7 years ago by
liuyang32201220
▴ 20
2
votes
2
replies
936
views
Double normalising when using sva and deseq2
DESeq2
Normalisation
Bulkrnaseq
Svaseq
18 months ago • updated 17 months ago
BioinfGuru
▴ 70
1
vote
2
replies
1.3k
views
Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
18 months ago
a_p
• 0
0
votes
1
reply
726
views
Can we compare 3 different experimental conditions with DESeq2?
DESeq2
StatisticalMethod
updated 18 months ago by
swbarnes2
★ 1.4k • written 18 months ago by
Esteban
• 0
0
votes
1
reply
642
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData
DESeq2
DifferentialExpression
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
ZhuYi
• 0
1
vote
2
replies
2.8k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 18 months ago by
rodrigo.duarte88
▴ 40 • written 6.1 years ago by
mohamedrefaat.1.1992
• 0
0
votes
1
reply
524
views
multiple condition issue running DESeq
DESeq2
updated 18 months ago by
Michael Love
43k • written 18 months ago by
Kelly
• 0
0
votes
3
replies
747
views
Ploting of normalized counts after batch removal
DESeq2
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
altuda
▴ 10
1
vote
1
reply
496
views
makeExampleDESeqDataSet using pilot data
DESeq2
updated 18 months ago by
Michael Love
43k • written 18 months ago by
li.d.peck
• 0
0
votes
2
replies
672
views
Best way to describe DEseq2 design
DESeq2
updated 18 months ago by
swbarnes2
★ 1.4k • written 18 months ago by
YouCook
• 0
1
vote
2
replies
824
views
Deseq2
DESeq2
rnaseqGene
updated 18 months ago by
Ram
▴ 220 • written 18 months ago by
Sudip
• 0
1
vote
1
reply
573
views
LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
boczniak767
▴ 740
0
votes
6
replies
1.2k
views
Counter-directional LFC shrinkage
DESeq2
updated 18 months ago by
Michael Love
43k • written 18 months ago by
ennui
• 0
0
votes
2
replies
1.2k
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
DESeq2
single-cell
scRNA
Pseudobulk
updated 18 months ago by
Guido Hooiveld
★ 4.1k • written 18 months ago by
Sara
• 0
0
votes
3
replies
2.0k
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 18 months ago by
Robert Castelo
★ 3.4k • written 18 months ago by
michelafrancesconi8
• 0
0
votes
2
replies
974
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2
clinicaltraits
Normalization
batchnormalisation
18 months ago
sukeshinik5
▴ 20
0
votes
4
replies
2.2k
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
tjl
• 0
1
vote
8
replies
1.3k
views
Slightly different count plots from R and spreadsheet
DESeq2
ggplot2
18 months ago
boczniak767
▴ 740
1
vote
3
replies
1.0k
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
boczniak767
▴ 740
0
votes
6
replies
1.6k
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
18 months ago
Ken C
• 0
2
votes
4
replies
1.1k
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 18 months ago by
Michael Love
43k • written 18 months ago by
shaunpeterson
• 0
4
votes
9
replies
1.4k
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
pangtaihin
• 0
0
votes
3
replies
787
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 18 months ago by
Michael Love
43k • written 18 months ago by
Kasper
• 0
0
votes
1
reply
765
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 18 months ago by
Michael Love
43k • written 18 months ago by
piemmea
• 0
0
votes
9
replies
2.3k
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 18 months ago by
BioinfGuru
▴ 70 • written 18 months ago by
Eric Katagirya
• 0
1
vote
2
replies
1.1k
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
18 months ago
BioinfGuru
▴ 70
0
votes
1
reply
627
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
sajadahmad41454
• 0
0
votes
1
reply
721
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
sajadahmad41454
• 0
2
votes
7
replies
2.0k
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
19 months ago
sajadahmad41454
• 0
2
votes
1
reply
836
views
Handling multiple differential expression comparisons
DESeq2
19 months ago • updated 17 months ago
Zainab
▴ 20
0
votes
6
replies
1.2k
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 19 months ago by
swbarnes2
★ 1.4k • written 19 months ago by
arfranco
▴ 130
2
votes
6
replies
2.3k
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 9 months ago by
Jane
• 0 • written 19 months ago by
Reza
• 0
0
votes
2
replies
526
views
DESeq2 v1.35.0
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
Espresso
• 0
0
votes
2
replies
904
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 months ago
kcarey
• 0
4,840 results • Page
5 of 97
Recent ...
Replies
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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