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
3
votes
5
replies
245
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
1 day ago
MedocRafael
• 0
4
votes
2
replies
707
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2
RNAseq
8 days ago • updated 1 day ago
mila
▴ 10
0
votes
3
replies
268
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 3 days ago by
ATpoint
★ 4.2k • written 3 days ago by
Mark
• 0
1
vote
4
replies
917
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
17 days ago • updated 4 days ago
Lucy
▴ 60
0
votes
3
replies
241
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
updated 16 days ago by
Gordon Smyth
51k • written 16 days ago by
Shaozhen
• 0
0
votes
0
replies
149
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution
rnaseqGene
RNAseq
29 days ago
JG13
• 0
0
votes
1
reply
211
views
Significant genes in DESeq2 analysis
DESeq2
RNASeq
updated 5 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
cbio
• 0
1
vote
9
replies
606
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 5 weeks ago by
James W. MacDonald
66k • written 6 weeks ago by
adrip
• 0
1
vote
3
replies
332
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 6 weeks ago by
James W. MacDonald
66k • written 6 weeks ago by
Ben
▴ 50
2
votes
2
replies
449
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 7 weeks ago by
jessica.mcclintock
• 0 • written 9 weeks ago by
ttt
• 0
0
votes
6
replies
783
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
9 weeks ago • updated 8 weeks ago
atan
• 0
2
votes
2
replies
289
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
9 weeks ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
139
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
9 weeks ago
Bibi
• 0
10
votes
11
replies
2.1k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 9 weeks ago by
Sara
• 0 • written 6.9 years ago by
Sylvain Foisy
▴ 80
1
vote
3
replies
402
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 10 weeks ago by
Gordon Smyth
51k • written 10 weeks ago by
Ashley
• 0
0
votes
3
replies
414
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 12 weeks ago by
ATpoint
★ 4.2k • written 12 weeks ago by
james.zhang20
• 0
0
votes
1
reply
270
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 3 months ago by
Michael Love
42k • written 3 months ago by
kcarey
• 0
0
votes
2
replies
288
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 3 months ago by
taur.vil
• 0
0
votes
2
replies
366
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
3 months ago
catv
• 0
5
votes
3
replies
492
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 11 weeks ago by
Gordon Smyth
51k • written 3 months ago by
Shaimaa Gamal
• 0
0
votes
1
reply
258
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 3 months ago by
Michael Love
42k • written 3 months ago by
09191919
• 0
0
votes
1
reply
236
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 3 months ago by
ATpoint
★ 4.2k • written 3 months ago by
Merav
• 0
0
votes
2
replies
485
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
4 months ago
kcarey
• 0
2
votes
2
replies
369
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
4 months ago
Sabiha
▴ 20
0
votes
2
replies
536
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
4 months ago
kcarey
• 0
1
vote
4
replies
421
views
DESeq2 Replicates
DESeq2
RNASeq
4 months ago
kcarey
• 0
1
vote
3
replies
488
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 4 months ago by
swbarnes2
★ 1.4k • written 4 months ago by
sap275
▴ 10
0
votes
4
replies
460
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
5 months ago • updated 4 months ago
mperalc
• 0
0
votes
2
replies
510
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 5 months ago by
Gordon Smyth
51k • written 5 months ago by
ryann
• 0
3
votes
5
replies
803
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 4 months ago by
Michael Love
42k • written 5 months ago by
sap275
▴ 10
2
votes
1
reply
356
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 5 months ago by
Michael Love
42k • written 5 months ago by
sap275
▴ 10
3
votes
6
replies
825
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
5 months ago
boczniak767
▴ 740
0
votes
0
replies
361
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
5 months ago
Abril
• 0
2
votes
2
replies
636
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
5 months ago
jackafiore
• 0
1
vote
2
replies
1.4k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 14 months ago by
informatician
• 0
0
votes
4
replies
545
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
5 months ago
candacenewcome
• 0
1
vote
3
replies
479
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
5 months ago
island
• 0
1
vote
3
replies
747
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 6 months ago by
georgii.vdovin
• 0
0
votes
1
reply
339
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 6 months ago by
Ram
▴ 210 • written 6 months ago by
Matvii Mykhailichenko
• 0
2
votes
4
replies
962
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
6 months ago
Sabiha
▴ 20
4
votes
6
replies
797
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 5 months ago by
Gordon Smyth
51k • written 6 months ago by
Shaimaa Gamal
• 0
3
votes
1
reply
429
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 6 months ago by
Gordon Smyth
51k • written 6 months ago by
Shaimaa Gamal
• 0
0
votes
3
replies
745
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 6 months ago by
Fayrouz
• 0
0
votes
1
reply
369
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
6 months ago
WS
• 0
2
votes
3
replies
1.7k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 7 months ago by
swbarnes2
★ 1.4k • written 7 months ago by
Bo
• 0
1
vote
2
replies
593
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
7 months ago
Sabiha
▴ 20
1
vote
2
replies
585
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
7 months ago
drewhaydensteele
• 0
7
votes
2
replies
1.1k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 7 months ago by
Gordon Smyth
51k • written 7 months ago by
annikagable
• 0
0
votes
3
replies
604
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
8 months ago • updated 7 months ago
Karthik
• 0
1
vote
1
reply
454
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 8 months ago by
Michael Love
42k • written 8 months ago by
pl23
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
Awards
• All
Popular Question
to
Lluís Revilla Sancho
▴ 730
Popular Question
to
maltethodberg
▴ 180
Scholar
to
Michael Love
42k
Popular Question
to
Leonardo Collado Torres
★ 1.1k
Scholar
to
Gordon Smyth
51k
Locations
• All
United States,
11 minutes ago
France,
16 minutes ago
United States,
19 minutes ago
WEHI, Melbourne, Australia,
38 minutes ago
United States,
40 minutes ago
Traffic: 669 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