Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
DEseq2
•
reset
2
votes
5
replies
2.3k
views
DESeq2 on CIRI results ?
deseq2
circrna
ciri
ciri2
7.6 years ago
sbcn
▴ 80
3
votes
7
replies
6.9k
views
Pre-filtering genes counts vs normalised counts DESeq2
deseq2
pre-filtering
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
bekah
▴ 40
1
vote
3
replies
1.4k
views
DESEq2: the use of interaction term and grouping with different betaPrior arguments in older version of DESEq2
deseq2
interaction term
multiple groups
betaprior
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
tarun2
• 0
1
vote
3
replies
1.5k
views
LRT results DESeq2
deseq2
Job
7.6 years ago
bekah
▴ 40
0
votes
1
reply
1.1k
views
DESeq2 design for time series data without "untreated"
deseq2
rnaseq
multiple time points
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
cecile.lorrain5
• 0
0
votes
2
replies
853
views
Comparing various genotypes to a control
deseq2
7.6 years ago
rattray56
• 0
2
votes
2
replies
8.1k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
deseq2
7.6 years ago
yueli7
▴ 20
2
votes
2
replies
2.4k
views
Deseq2 alternative splicing in understudied organism
deseq2
splicing
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
yannickwurm
• 0
1
vote
1
reply
1.5k
views
Generating RPKM data from dds (DESeq2 pipeline)
deseq2
dds
RPKM
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
harry.horsnell.17
• 0
0
votes
5
replies
1.7k
views
DEseq2 differentially expressed genes have lower expression values than non-differentially expressed genes
deseq2
R
7.6 years ago
lychen83
• 0
1
vote
8
replies
5.1k
views
DESeq2: betaPrior changes significance dramatically
deseq2
betaPrior
shrinkage
significance
7.6 years ago
brynedal
▴ 40
0
votes
13
replies
2.2k
views
Artificial P-value caused by outlier samples
deseq2
written 7.6 years ago by
Xianjun Dong
▴ 10
2
votes
5
replies
1.4k
views
trouble in install DESeq2
deseq2
package installation
7.6 years ago
yueli7
▴ 20
0
votes
8
replies
2.8k
views
inter-species RNA-seq with DEseq2: how to account for gene length differences
deseq2
normalization
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
akozlenkov
• 0
0
votes
1
reply
1.0k
views
DESeq2: Multifactor design working with example data but not with my data
deseq2
multiple factor design
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
1992
▴ 10
1
vote
2
replies
1.6k
views
Study design in DESeq2
deseq2
Model matrix not full rank
model.matrix
study design
7.6 years ago
Krzysztof Kolmus
▴ 10
4
votes
3
replies
1.6k
views
DESeq2 why estimate dispersion on log scale
deseq2
dispersoin
estimatedispersions
written 7.6 years ago by
xr2120
• 0
0
votes
3
replies
1.5k
views
Analyzing a subgroups of samples, which result should I trust
deseq2
rna-seq
written 7.6 years ago by
Raymond
▴ 20
1
vote
1
reply
1.2k
views
Post-processing RNA-Seq after tximport
salmon rna seq
tximport
ruv-seq
deseq2
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
mad6kj
• 0
1
vote
5
replies
2.0k
views
p-value the same for different contrasts DESeq2
deseq2
design and contrast matrix
updated 9 months ago by
caroline.zanchi
▴ 10 • written 7.6 years ago by
chitsazanalex
▴ 10
1
vote
2
replies
546
views
OTU versus Sequence in Test Results Table
deseq2
7.6 years ago
irene.yang
▴ 10
0
votes
1
reply
939
views
Identifying ago2 enriched genes under 2 different conditions
DESeq2
RIP
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
anurupadevi
• 0
1
vote
2
replies
4.2k
views
dyld: Library not loaded: @rpath/libc++abi.1.dylib
DESeq2
biocLite
updated 7.6 years ago by
Mike Smith
★ 6.6k • written 7.6 years ago by
jordan.berg
• 0
1
vote
5
replies
1.7k
views
Comparing RNA-Seq expression data from different sequencers (HiSeq3000 and NovaSeq6000) - are there methods for batch effect corrections?
deseq2
rna-seq
illumina
batch effect
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
JP Cartailler
▴ 40
0
votes
1
reply
997
views
RNAseq DESeq2 paired data design help
rnaseq
design matrix
deseq2
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
umlch
• 0
0
votes
3
replies
1.6k
views
Group comparison using DESeq
deseq2
multiple groups
updated 7.6 years ago by
James W. MacDonald
68k • written 7.6 years ago by
amir_b_e
• 0
32
votes
16
replies
21k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 7.6 years ago by
luxeredias
▴ 20 • written 9.4 years ago by
tangming2005
▴ 200
0
votes
1
reply
814
views
How to use normalized DESeq2 data for downstream analysis?
deseq2
normalization
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
Arying
• 0
3
votes
1
reply
26k
views
DESEQ2, VST PCA/Clustering: Is it not advisable to standard normalize data?
deseq2
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
owen.whitley
▴ 10
1
vote
3
replies
1.7k
views
Information regarding the (minimum) number of genes needed to analyse with DESeq2
deseq2
7.6 years ago
suranandbabu85
• 0
1
vote
3
replies
943
views
Differentially expressed genes detection between three classes with a batch effect in DESeq2
deseq2
batch effect
differential gene expression
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
francesco.tabaro
• 0
1
vote
3
replies
1.6k
views
Results counts post DESeq same raw counts
DESeq2
results
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
A
▴ 60
2
votes
4
replies
2.4k
views
DESeq2 with multi level
deseq2
lfcshrink
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
pierre.k
• 0
1
vote
2
replies
2.4k
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2
PCA
rlog transformation
biotype
7.6 years ago
JoannaF
▴ 10
1
vote
2
replies
9.4k
views
DESEQ2 design with multiple conditions
deseq2
design matrix
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
vrehaman
• 0
0
votes
3
replies
1.2k
views
interaction model deseq2 specific DE genes
deseq2
interaction model
differential expression
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
aec
▴ 90
1
vote
8
replies
1.5k
views
Unexpected differences in results from paired analysis with DESeq2
DESEq2
paired analysis
factor levels
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
luisa.bresadola
• 0
0
votes
1
reply
1.1k
views
DESeq2 - Test for linear combinations
deseq2
linear combination
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
xavi
• 0
4
votes
6
replies
9.8k
views
DESeq2 Error in varianceStabilizingTransformation
deseq2
updated 7.6 years ago by
kasia_piwosz
• 0 • written 11.1 years ago by
mfarhi
▴ 10
1
vote
1
reply
586
views
miRNA DE analysis using DeSeq2
deseq2
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
sehjpal.madhu
▴ 10
2
votes
3
replies
1.1k
views
Understand how DESeq estimates SE for log2 fold change
deseq2
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
mt1022
• 0
1
vote
10
replies
1.8k
views
Allele-specific expression with different gene lenghts
deseq2
allele-specific-expression
rnaseq
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
gtechbio
▴ 10
0
votes
13
replies
7.9k
views
DESeq2: Poor dispersion fit, even when a local or custom fit is used
deseq2
dispersion
7.6 years ago
Frederik Ziebell
▴ 30
0
votes
2
replies
871
views
normalisation of count data
deseq2
updated 7.6 years ago by
Ryan C. Thompson
★ 7.9k • written 7.6 years ago by
sara.beier
• 0
0
votes
2
replies
1.4k
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2
design and contrast matrix
multiple factor design
design matrix
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
khhsource
• 0
0
votes
4
replies
1.9k
views
colData and design problem
deseq2
7.6 years ago
soheilazareie
• 0
0
votes
2
replies
1.4k
views
tech replicates or bio replicate?
deseq2
updated 7.6 years ago by
williamgeorge51547
• 0 • written 7.7 years ago by
Xianjun Dong
▴ 10
0
votes
1
reply
613
views
DESeq2 (Different results when using interactive term equation)
DESeq2
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
LR0306
▴ 10
4
votes
8
replies
8.0k
views
Convert Normalized RNA-Seq counts to TPM after Batch Correction
sva
deseq2
limma
updated 3.3 years ago by
eve.olszanowski
• 0 • written 7.7 years ago by
rrcutler
▴ 70
1
vote
2
replies
1.6k
views
deseq2 normalization with metagenomics data
deseq2
updated 7.7 years ago by
Levi Waldron
★ 1.1k • written 7.7 years ago by
David
▴ 860
4,840 results • Page
64 of 97
Recent ...
Replies
Comment: 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
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.
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
Awards
• All
Popular Question
to
shepherl
4.2k
Popular Question
to
Gordon Smyth
53k
Popular Question
to
k___
▴ 30
Popular Question
to
efoss
▴ 10
Popular Question
to
James W. MacDonald
68k
Locations
• All
United States,
26 minutes ago
The city by the bay,
29 minutes ago
United States,
35 minutes ago
United States,
1 hour ago
United States,
1 hour ago
Traffic: 1129 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6