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DEseq2
•
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0
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0
replies
594
views
Best practice for comparing a subset of data /
DESeq2
2.7 years ago
TzuChiao
▴ 10
5
votes
15
replies
2.8k
views
how can I do gene differential analysis on data after vst
DESeq2
written 2.7 years ago by
linouhao
▴ 20
0
votes
1
reply
1.1k
views
what does "exp1" mean in the gage() function?
gage
clusterProfiler
DESeq2
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
m-bihie
▴ 10
2
votes
2
replies
1.3k
views
Multifactorial Design for DESEQ2
DESeq2
rna-seq
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
genome_nerd
• 0
3
votes
2
replies
1.5k
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2
apeglm
2.7 years ago • updated 2.6 years ago
Daphnia
• 0
0
votes
2
replies
2.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.7 years ago
Giulia
• 0
2
votes
3
replies
3.6k
views
deseq2 normalization and statistical method
normalization
deseq2
StatisticalMethod
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
SH
▴ 10
0
votes
0
replies
832
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.7 years ago
Giulia
• 0
1
vote
2
replies
1.8k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2
RNAseq
RUVSeq
2.7 years ago
garbuzov
• 0
0
votes
6
replies
1.2k
views
DispEsts plot
DESeq2
2.7 years ago
Sep
• 0
4
votes
4
replies
1.6k
views
Can I run DESeq2 with SMART-Seq data
DESeq2
SMART-seq
2.7 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
1
reply
805
views
Are polynomial contrasts for a time factor possible in DESeq2?
DESeq2
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
dairey
▴ 10
0
votes
1
reply
794
views
deseq2 nested multifactorial analysis
DESeq2
multifactorial
nested
updated 2.7 years ago by
Basti
▴ 780 • written 2.7 years ago by
jd
• 0
0
votes
2
replies
1.0k
views
Help understanding dispersion values and why so many genes change significance after removing low read samples
DESeq2
2.7 years ago • updated 2.6 years ago
Miriam
• 0
0
votes
1
reply
2.2k
views
DESeqDataSetFromMatrix NA values
DESeq2
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
hyejo
• 0
1
vote
3
replies
1.3k
views
How to compute(calculate) rlog and vst provided from DESeq2
DESeq2
2.7 years ago
tstpp
• 0
1
vote
2
replies
749
views
DESeq2 pvalues overly conservative
DESeq2
2.7 years ago
gdolsten
▴ 10
2
votes
1
reply
2.0k
views
deseq2 RLE normalization
RLE
normalization
deseq2
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
SH
▴ 10
0
votes
1
reply
1.2k
views
Using DESeq2 only for normalization
DESeq2
Normalization
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
phmai1148
• 0
0
votes
3
replies
1.1k
views
Does it make sense to have so many statistically significant gene differentially expressed after DESeq2 paired sample analysis?
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Sep
• 0
5
votes
7
replies
1.7k
views
different number of DEG because of outliers
DESeq2
RNASeq
updated 22 months ago by
Gordon Smyth
53k • written 2.7 years ago by
Ilya
• 0
1
vote
2
replies
826
views
colData design issues, need help in R
DESeq2
2.7 years ago
R_diot
• 0
0
votes
2
replies
755
views
DESeq2 paramter inference
DESeq2
2.7 years ago
BioEpi
• 0
0
votes
1
reply
747
views
processing samples with significantly different counts
DESeq2
Normalization
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
Anastasiia
• 0
0
votes
5
replies
2.3k
views
DESeq Normalization and miRNAs Filtering
DESeq2
Normalization
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
phmai1148
• 0
0
votes
1
reply
592
views
DESeq2 design for time series and control-treated groups
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
T.RU
• 0
0
votes
7
replies
2.2k
views
DESeq2 Log fold change strange values for certain genes
DESeq2
2.7 years ago
Layla
• 0
0
votes
1
reply
614
views
Time-course for three-factor design
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
boczniak767
▴ 740
0
votes
2
replies
898
views
DESeq2 with temporal data and different treatments
DESeq2
updated 2.7 years ago by
swbarnes2
★ 1.4k • written 2.7 years ago by
T.RU
• 0
0
votes
1
reply
927
views
DESeq2 won't load
DESeq2
load
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Naomi
• 0
1
vote
1
reply
880
views
Accounting for breadth of coverage while using DESeq2
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Peter
• 0
0
votes
3
replies
815
views
DESeq2 for another layer of differential analysis
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Ming
• 0
0
votes
1
reply
727
views
Use of DESeq given unusual experimental data
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
GLFrey
• 0
0
votes
7
replies
1.2k
views
Does the running time of DESeq function is much more longer for design factor containing two variable compare to design factor containing only one v…
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Sep
• 0
1
vote
2
replies
1.2k
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2
limma
edgeR
RSEM
2.7 years ago
Yang Shi
▴ 10
3
votes
5
replies
1.2k
views
Horizontal integration of two RNA-seq datasets derived from two different platforms
DESeq2
dataIntegration
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
rjoana
• 0
2
votes
3
replies
1.8k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
suphamon.j
▴ 20
4
votes
5
replies
2.9k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2
edgeR
scRNAseq
updated 2.7 years ago by
Peter Hickey
▴ 760 • written 2.7 years ago by
EspressoKris
▴ 10
0
votes
1
reply
1.0k
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
marslena
• 0
1
vote
3
replies
989
views
DESeq2 check failure on Linux ARM64
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
martin.grigorov
▴ 10
3
votes
10
replies
5.4k
views
Is there any chance to solve "the model matrix is not full rank" in DESeq2?
DESeq2
2.7 years ago
Sep
• 0
0
votes
1
reply
1.4k
views
Which samples to remove from analysis based on Cook's distance outliers plot
DESeq2
cooks
outliers
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
Michael
• 0
1
vote
8
replies
2.3k
views
Understandig listValues argument of DESEQ in multiple group comparisons
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 3.8 years ago by
User000
• 0
1
vote
1
reply
956
views
Subsetting DESeq when different cell types
DESeq2
RNASeq
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
andrebolerbarros
▴ 20
1
vote
2
replies
1.0k
views
ColData not reading properly
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
wgodfre1
• 0
0
votes
2
replies
1.1k
views
DESeq2 replicates in time course data
DESeq2
timecoursedata
replicates
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
fepesanz8
• 0
1
vote
4
replies
1.5k
views
How do I design my DESEQ experiment?
DESeq2
Metagenomics
2.7 years ago
Michael
• 0
0
votes
2
replies
1.5k
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2
Galaxy
pca
updated 2.7 years ago by
swbarnes2
★ 1.4k • written 2.7 years ago by
mbxdn1
• 0
0
votes
7
replies
2.3k
views
Weird dispersion and volcano plots in DEA with paired samples
DESeq2
RNASeq
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
lara
• 0
0
votes
3
replies
1.4k
views
PCA subset of genes vs DE
DESeq2
RNASeq
written 2.7 years ago by
andrebolerbarros
▴ 20
4,839 results • Page
14 of 97
Recent ...
Replies
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"]) ```
Answer: p.adjust BH Question
by
Gordon Smyth
53k
Duplicate of https://support.bioconductor.org/p/41077/
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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