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 :
RnaSeq
•
reset
0
votes
2
replies
134
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
8 days ago • updated 7 days ago
kcarey
• 0
2
votes
2
replies
191
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
15 days ago • updated 14 days ago
Sabiha
▴ 20
0
votes
2
replies
163
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
15 days ago • updated 14 days ago
kcarey
• 0
1
vote
4
replies
235
views
DESeq2 Replicates
DESeq2
RNASeq
22 days ago
kcarey
• 0
1
vote
3
replies
261
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 24 days ago by
swbarnes2
★ 1.3k • written 27 days ago by
sap275
▴ 10
0
votes
4
replies
219
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
4 weeks ago • updated 28 days ago
mperalc
• 0
0
votes
2
replies
209
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
ryann
• 0
3
votes
5
replies
545
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 24 days ago by
Michael Love
41k • written 4 weeks ago by
sap275
▴ 10
2
votes
1
reply
200
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
sap275
▴ 10
3
votes
6
replies
427
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
5 weeks ago
boczniak767
▴ 720
0
votes
0
replies
156
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
6 weeks ago
Abril
• 0
2
votes
2
replies
283
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
7 weeks ago
jackafiore
• 0
1
vote
2
replies
999
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 10 months ago by
informatician
• 0
0
votes
4
replies
313
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
8 weeks ago
candacenewcome
• 0
1
vote
3
replies
290
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
8 weeks ago
island
• 0
1
vote
3
replies
492
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 9 weeks ago by
georgii.vdovin
• 0
0
votes
1
reply
178
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 9 weeks ago by
Ram
▴ 190 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
4
replies
457
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
9 weeks ago
Sabiha
▴ 20
4
votes
6
replies
492
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 7 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Shaimaa Gamal
• 0
3
votes
1
reply
217
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Shaimaa Gamal
• 0
0
votes
3
replies
367
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 11 weeks ago by
Fayrouz
• 0
0
votes
1
reply
219
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
11 weeks ago
WS
• 0
2
votes
3
replies
981
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 3 months ago by
swbarnes2
★ 1.3k • written 3 months ago by
Bo
• 0
1
vote
2
replies
367
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
1
vote
2
replies
372
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
3 months ago
drewhaydensteele
• 0
7
votes
2
replies
625
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annikagable
• 0
0
votes
3
replies
402
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
4 months ago • updated 3 months ago
Karthik
• 0
1
vote
1
reply
336
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 4 months ago by
Michael Love
41k • written 4 months ago by
pl23
• 0
2
votes
3
replies
396
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
4 months ago
Karthik
• 0
2
votes
2
replies
356
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
4 months ago
Manthos
• 0
2
votes
4
replies
547
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
4 months ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
393
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 4 months ago by
Michael Love
41k • written 5 months ago by
Sean
• 0
0
votes
2
replies
469
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 4 months ago by
Leonardo Collado Torres
★ 1.0k • written 5 months ago by
tangming2005
▴ 190
0
votes
9
replies
2.4k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 4 months ago by
blowfish
• 0 • written 6.4 years ago by
bharata1803
▴ 60
1
vote
4
replies
552
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
4 months ago
Wending
• 0
0
votes
0
replies
309
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
5 months ago
mch
• 0
4
votes
2
replies
523
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
alvaroperona1
▴ 10
0
votes
6
replies
731
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
5 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
287
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
5 months ago
Sara
• 0
0
votes
2
replies
588
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
5 months ago
Karthik
• 0
0
votes
0
replies
237
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
5 months ago
Florian
• 0
0
votes
0
replies
295
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
5 months ago
Xinqi
• 0
0
votes
0
replies
287
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
5 months ago
Sara
• 0
1
vote
1
reply
356
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
fuqichen1
• 0
1
vote
7
replies
744
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 3 months ago by
Gordon Smyth
50k • written 5 months ago by
Gimena
• 0
0
votes
2
replies
379
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality
RNASeq
DESeq2
updated 5 months ago by
swbarnes2
★ 1.3k • written 5 months ago by
Jules
• 0
0
votes
1
reply
364
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
updated 5 months ago by
Basti
▴ 750 • written 6 months ago by
Luke
• 0
3
votes
5
replies
727
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
Shashank
• 0
1
vote
1
reply
410
views
bulk RNA-Seq batch correction
RNASeqData
rnaseqcomp
RNASeq
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
jg0428
• 0
0
votes
1
reply
520
views
DESeq design and contrast with multiple factors
RNASeq
DESeq2
updated 6 months ago by
Michael Love
41k • written 6 months ago by
Adam
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Awards
• All
Popular Question
to
michael.s
• 0
Popular Question
to
James W. MacDonald
65k
Popular Question
to
Pierre Lindenbaum
▴ 10
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Jenny Drnevich
★ 2.0k
Locations
• All
Mexico,
2 minutes ago
United States,
19 minutes ago
United States,
2 hours ago
Ghana/KNUST,
2 hours ago
Canada,
4 hours ago
Traffic: 558 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