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DEseq2
•
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0
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834
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Complex design in DESeq2 doesn't seem to be supported in Glimma
limma
Glimma
RNASeq
DESeq2
3.9 years ago
Jonas
• 0
0
votes
2
replies
1.5k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 3.9 years ago by
Steve Lianoglou
★ 13k • written 3.9 years ago by
Jonas
• 0
0
votes
3
replies
1.7k
views
Is it possible to specify random nested factor in DEseq2?
nested
DESeq2
updated 3.8 years ago by
Michael Love
43k • written 3.9 years ago by
yampolsk
• 0
2
votes
2
replies
5.1k
views
EdgeR installation issue
limma
edgeR
DESeq2
3.9 years ago
aonghus
• 0
0
votes
2
replies
1.7k
views
sigh of log2FC values in DESeq2
sign
FoldChange
DESeq2
reference
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
yampolsk
• 0
3
votes
2
replies
1.8k
views
Ashr and IHW
Ashr
LFCShrinkage
IHW
DESeq2
3.9 years ago
Bex
• 0
2
votes
9
replies
6.2k
views
Deseq2 normalization for WGCNA
RNASeq
Deseq2
DESeq2
WGCNA
updated 3.6 years ago by
Michael Love
43k • written 3.9 years ago by
jms2520
▴ 10
0
votes
2
replies
1.3k
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions
design
DESeq2
Synergy
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
johannesdolberg
• 0
4
votes
4
replies
3.5k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 24 months ago by
Gordon Smyth
53k • written 4.0 years ago by
mohammedtoufiq91
▴ 10
3
votes
2
replies
1.1k
views
P-values change 100-fold with only a single count changed
DESeq2
4.0 years ago • updated 3.9 years ago
Andrey
• 0
0
votes
1
reply
1.3k
views
Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta
UseMethod("filter_")
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
dmbergau
• 0
0
votes
2
replies
1.7k
views
DESeqDataSet design issue
DESeq
DESeq2
4.0 years ago
matthew.valentine
• 0
2
votes
1
reply
1.7k
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST
Tumor-Purity
VST
DESeq2
Normalization
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
Bioinf_sc
• 0
0
votes
1
reply
1.0k
views
RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
RNASeq
DESeq2
airway
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
dmbergau
• 0
3
votes
3
replies
2.6k
views
DESeq2 - batch, condition and tissue information
DESeq2
4.0 years ago
Ela__77
▴ 10
0
votes
9
replies
2.6k
views
DESeq2 analyze MeRIP-seq
DESeq2
MeRIP-seq
updated 3.1 years ago by
Michael Love
43k • written 4.0 years ago by
BioEpi
• 0
1
vote
2
replies
2.0k
views
Design formula in DESeq2
groups
dispersion
DESeq2
desing
4.0 years ago
m.glymenaki
• 0
3
votes
4
replies
1.4k
views
DESEQ2 Results log2fold and pvalue changes after removing genes
DESeq2
4.0 years ago
Bine
▴ 50
0
votes
1
reply
930
views
different results between DESeq model with multiple groups or with specific groups
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
giulia.lopatriello
• 0
0
votes
1
reply
1.2k
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast
design
DESeq2
continuous
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
tiansy
• 0
0
votes
3
replies
3.1k
views
Error in DESeq2
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
mithu18mohan
• 0
0
votes
2
replies
1.2k
views
deseq2 datasetfrommatrix
DESeq2
updated 4.0 years ago by
ATpoint
★ 5.0k • written 4.0 years ago by
Chay
• 0
1
vote
1
reply
1.2k
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment
RNASeq
design
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
Kesava
• 0
0
votes
9
replies
2.5k
views
DEseq2 replicate normalization
DEseq2
replicate
DESeq2
normalization
4.0 years ago
michael.morash
• 0
3
votes
5
replies
5.7k
views
Can I use VST on TPM data? (DESeq2)
DESeq2
VST
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
BT
▴ 10
0
votes
1
reply
2.0k
views
values (NA) in p value Deseq2 (reopen)
pvalue
NA
R
DESeq2
updated 4.0 years ago by
ATpoint
★ 5.0k • written 4.0 years ago by
Johan Largo
• 0
2
votes
2
replies
1.1k
views
padjust after running DESEQ2
DESeq2
4.0 years ago
Bine
▴ 50
0
votes
4
replies
5.1k
views
Normalization by variance stabilizing transformation VST
library
composition
vst
DESeq2
Normalization
4.0 years ago
kristoffersandas
• 0
0
votes
4
replies
1.8k
views
normalizing EXOM-seq read using DESeq2
ExomeSeq
DESeq2
4.0 years ago
adR
▴ 40
0
votes
2
replies
1.2k
views
Troubleshooting DESeq2 Analysis: no DE genes found in subset
DESeq2
updated 4.0 years ago by
swbarnes2
★ 1.4k • written 4.0 years ago by
Sophie Nicole
• 0
10
votes
23
replies
16k
views
Macbook M1 install genefilter failed
DESeq2
m1
macbook
genefilter
4.3 years ago • updated 3.1 years ago
soda
▴ 80
1
vote
4
replies
2.7k
views
DESeq2 - VST data
DESeq2
VST
4.0 years ago
AP
• 0
1
vote
1
reply
1.2k
views
betaPrior and lfcShrink
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
shepherd.forjesus
• 0
0
votes
1
reply
1.6k
views
Calculating gene expression dominance coefficient via DESeq2
RNASeq
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
Philipp.kaufmann
• 0
0
votes
1
reply
1.2k
views
DESeq2: Difference between two groups of conditions
factor
DESeq2
MultipleComparison
updated 4.0 years ago by
swbarnes2
★ 1.4k • written 4.0 years ago by
diegocastano182
• 0
0
votes
8
replies
2.3k
views
Annotating DESeq2 Differential Expression Results
biomaRt
DESeq2
4.0 years ago
adeler001
• 0
6
votes
4
replies
2.3k
views
Which rlog should I use for DESeq2 analysis
samples
rlog
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
rafaelsolersanblas
▴ 50
0
votes
5
replies
2.0k
views
95% confidence intervals for PCA in DESEQ2
DESEQ2
DESeq2
4.0 years ago
tylerdodgeball2019
• 0
0
votes
3
replies
926
views
Which interactions terms to choose?
interac
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
יהב
• 0
0
votes
6
replies
1.7k
views
DESeq2 log2Foldchange issue
DESeq2
4.0 years ago
Cheryl
• 0
0
votes
1
reply
1.1k
views
Variation in number of DEGs on LFC shrinkage
DESeq2
lfcShrink
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
Deevanshu
• 0
0
votes
3
replies
1.1k
views
Complex Contrast in DESeq2
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
bioinformaticssrm2011
• 0
0
votes
2
replies
1.5k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions
design
Multifactorial
DESeq2
updated 4.1 years ago by
swbarnes2
★ 1.4k • written 4.1 years ago by
Marie
• 0
0
votes
5
replies
1.7k
views
Is there a way to get the confidence interval for the fold change generated on DESeq2
DESeq2
4.1 years ago • updated 4.0 years ago
adeler001
• 0
0
votes
1
reply
888
views
DESeq2 Timecourse design
DESeq2
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
Mallory
▴ 10
3
votes
5
replies
2.5k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta
SummarizedExperiment
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.1 years ago by
alexw
• 0
0
votes
1
reply
963
views
Account for parent cell line when comparing isogenic mutants
interactions
design
DESeq2
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
oliver.ziff
• 0
6
votes
10
replies
2.4k
views
rnaseqGene: Different output when generating step by step airway dataset
tximeta
DESeq2
rnaseqGene
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
jorgeplaza
▴ 20
0
votes
1
reply
1.3k
views
DESeq2 design formula
DESeq2
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
nikolaus.virgolini
• 0
0
votes
2
replies
1.6k
views
Design formula in DESeq2
model
BatchEffect
hidden
Design
DESeq2
4.1 years ago
m.glymenaki
• 0
4,839 results • Page
25 of 97
Recent ...
Replies
Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
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
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
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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