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rnaseqdata
•
reset
1
vote
3
replies
1.6k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
2.9 years ago
dantasezequiel1
• 0
2
votes
3
replies
1.3k
views
RNA-seq analysis without replicates
DESeq2
RESEQ
RNASeqData
updated 11 months ago by
Cynthia
• 0 • written 11 months ago by
4214811
• 0
0
votes
2
replies
596
views
Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma
RNASeqData
edgeR
updated 12 months ago by
Hilary
▴ 30 • written 12 months ago by
Lucas
• 0
1
vote
7
replies
742
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
1
vote
2
replies
998
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 10 months ago by
informatician
• 0
1
vote
2
replies
2.3k
views
Understanding how to contrast two treatments in DESeq2
DESeq2
RNASeqData
updated 19 months ago by
swbarnes2
★ 1.3k • written 19 months ago by
Jennifer M
• 0
3
votes
6
replies
1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2
RNASeqData
DifferentialExpression
updated 3.3 years ago by
Michael Love
41k • written 3.3 years ago by
Ben
▴ 50
0
votes
10
replies
2.8k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer
RNAseqData
GenomicFeatures
Cancer
RNAseqData
GenomicFeatures
updated 9.7 years ago by
Fong Chun Chan
▴ 320 • written 9.7 years ago by
Valerie Obenchain
★ 6.8k
0
votes
1
reply
736
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq
RNASeqData
limma
limmaGUI
updated 24 months ago by
Michael Love
41k • written 24 months ago by
sushimoto
• 0
0
votes
6
replies
716
views
Questionable limma results for differential expression on RNA-seq
RNASeqData
DifferentialExpression
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
gld-bioinf
• 0
0
votes
1
reply
1.0k
views
RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2
multiple factor design
rnaseqdata
updated 8.0 years ago by
Michael Love
41k • written 8.0 years ago by
Dimitris Polychronopoulos
▴ 80
0
votes
5
replies
2.1k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData
isoform
DESeq2
23 months ago • updated 22 months ago
priyanka.m
• 0
6
votes
4
replies
10k
views
How to use combat in order to remove batch effects?
BatchEffect
DESeq2
RNASeqData
updated 2.2 years ago by
BioNovice247
• 0 • written 3.0 years ago by
Emma
▴ 10
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.0 years ago
hgalmoore
• 0
2
votes
4
replies
2.7k
views
Compare 3 RNASeq groups with no control in DESeq2
anova
RNASeqData
tukeyTest
DESeq2
3.4 years ago • updated 3.3 years ago
ecg1g15
▴ 20
0
votes
1
reply
588
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
khaserdene99
• 0
0
votes
1
reply
522
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData
DESeq2
updated 8 months ago by
Michael Love
41k • written 8 months ago by
Abhishek Singh
▴ 20
0
votes
3
replies
698
views
Understanding edgeR differential expression results
Transcriptomics
edgeR
DifferentialExpression
RNASeqData
RNASeq
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Teresa
• 0
0
votes
2
replies
1.3k
views
How to run vst transformation
RNASeqData
vst
updated 22 months ago by
Michael Love
41k • written 23 months ago by
sropri
• 0
0
votes
1
reply
599
views
HSMMSingleCell metadata
ExperimentHubData
ExpressionData
CellDataSet
RNASeqData
2.0 years ago
karl.stamm
▴ 10
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 13 months ago by
Rebekah
• 0
0
votes
2
replies
591
views
RNA-Seq and disease outcome analysis
rnaseqAnalysis
RNASeqData
13 months ago
JonasEnder
• 0
3
votes
2
replies
894
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData
DEGreport
edgeR
3.1 years ago
Wuschel
▴ 10
22
votes
15
replies
7.2k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 4 months ago by
Marie
▴ 10 • written 23 months ago by
Dina
▴ 50
1
vote
1
reply
614
views
Strange error while running DESeq() function.
DESeq2
RNASeq
RNASeqData
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
treebig44
▴ 30
4
votes
3
replies
1.1k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2
idep
RNASeqData
updated 2.1 years ago by
swbarnes2
★ 1.3k • written 2.1 years ago by
student2
▴ 10
0
votes
2
replies
283
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
3 months ago
Luca
• 0
0
votes
1
reply
540
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2
RNASeqData
DifferentialExpression
updated 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
Julie
• 0
1
vote
1
reply
547
views
DESEQ2 differential expression for subsets of data?
RNASeqData
DESeq2
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
amnahsiddiqa
▴ 10
1
vote
1
reply
376
views
Deseq contrast question
RNASeqData
DESeq2
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Hannah
▴ 10
1
vote
2
replies
1.5k
views
Binning expression data along with capturing gene identifiers
rnaseqdata
clustering
updated 9.2 years ago by
Johannes Rainer
★ 2.0k • written 9.2 years ago by
Alan Smith
▴ 150
2
votes
4
replies
1.1k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData
DESeq2
2.6 years ago
khaveh
▴ 10
2
votes
8
replies
2.2k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Rishav
▴ 20
0
votes
2
replies
740
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR
DEGs
DESEQ2
RNASeqData
2.1 years ago
Raito92
▴ 60
1
vote
2
replies
480
views
I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData
DESeq2
updated 8 months ago by
Michael Love
41k • written 8 months ago by
mohammad.hossein.banabazi
• 0
1
vote
4
replies
997
views
lncRNA Differential Expression Analysis
DESeq2
limma
RNASeqData
24 months ago
sushimoto
• 0
0
votes
4
replies
589
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
sohail.mbio
▴ 10
0
votes
6
replies
1.1k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
3.0 years ago
Rishav
▴ 20
1
vote
5
replies
315
views
RLE plots before and after RUVg correction are the same
RUVSeq
RUVcorr
RNASeqData
BatchEffect
DifferentialExpression
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Shaimaa Gamal
• 0
2
votes
9
replies
2.1k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
21 months ago
Peipei
• 0
1
vote
4
replies
1.2k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
14 months ago
Iwan
• 0
3
votes
3
replies
1.3k
views
How to formulate 2 factor nested design in DESeq2
nested_design
RNASeqData
DESeq2
22 months ago
JK Kim
▴ 20
1
vote
6
replies
1.3k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData
DESeq2
rnaseqGene
3.1 years ago
Seaweed
• 0
5
votes
6
replies
478
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
9 weeks ago
Shaimaa Gamal
• 0
1
vote
1
reply
1.1k
views
Help understanding edgeR code for doing exactTest
exacttest
RNASeqData
edgeR
diffGeneAnalysis
updated 2.4 years ago by
Gordon Smyth
50k • written 2.4 years ago by
Julia
• 0
1
vote
1
reply
277
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
kaurprab
• 0
1
vote
2
replies
615
views
Installation of R-packages for RNA-seq analysis
RNASeqData
13 months ago
Begin-R
• 0
0
votes
3
replies
602
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
4 months ago
Oenone
• 0
8
votes
2
replies
6.5k
views
handling outliers with DESeq2
RNASeqData
DESeq2
Outliers
2.9 years ago
paty
▴ 60
7
votes
5
replies
3.3k
views
Normalise to a housekeeping gene in DESEq2
DESeq2
housekeeping
R
RNASeqData
3.3 years ago
ecg1g15
▴ 20
50 results • Page
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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
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