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Showing :
rnaseqdata
•
reset
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
15
replies
2.4k
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
3.0 years ago • updated 2.9 years ago
demisa
• 0
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
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
9
replies
814
views
DESeq2 not replicable results
RNASeqData
DESeq2
updated 8 months ago by
Michael Love
41k • written 8 months ago by
Matteo
• 0
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
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
7
replies
1.5k
views
DESeqDataSetFromMatrix error
BiocGenerics
DESeq2
DEGreport
RNASeqData
DEG
updated 20 months ago by
James W. MacDonald
65k • written 20 months ago by
Diya
• 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
2
votes
6
replies
8.4k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2
RNASeq
RNASeqData
2.0 years ago
treebig44
▴ 30
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
0
votes
6
replies
715
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
6
replies
1.1k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
3.0 years ago
Rishav
▴ 20
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
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
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
7
votes
5
replies
3.3k
views
Normalise to a housekeeping gene in DESEq2
DESeq2
housekeeping
R
RNASeqData
3.3 years ago
ecg1g15
▴ 20
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq
RNASeqData
updated 21 months ago by
ATpoint
★ 4.0k • written 21 months ago by
Sanatan
• 0
3
votes
5
replies
543
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 24 days ago by
Michael Love
41k • written 4 weeks ago by
sap275
▴ 10
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.0 years ago
hgalmoore
• 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
2
votes
4
replies
596
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
6 months ago
Shihui
• 0
0
votes
4
replies
986
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano
RNASeqData
DifferentialExpression
10 months ago
ruba-mahmoud
• 0
2
votes
4
replies
1000
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 4 months ago by
melissawimmer219
• 0 • written 9 months ago by
zxc741xb
• 0
1
vote
4
replies
1.2k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
14 months ago
Iwan
• 0
2
votes
4
replies
2.7k
views
Compare 3 RNASeq groups with no control in DESeq2
anova
RNASeqData
tukeyTest
DESeq2
3.3 years ago
ecg1g15
▴ 20
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
3
votes
4
replies
476
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
4 months ago
pl23
• 0
1
vote
4
replies
996
views
lncRNA Differential Expression Analysis
DESeq2
limma
RNASeqData
24 months ago
sushimoto
• 0
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
1
vote
3
replies
287
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
8 weeks ago
island
• 0
2
votes
3
replies
1.0k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
amnahsiddiqa
▴ 10
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
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
3
votes
3
replies
826
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq
RNASeqData
sva
limma
9 months ago
amnahsiddiqa
▴ 10
0
votes
3
replies
601
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
4 months ago
Oenone
• 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport
tx2gene
rnas
DESeq2
RNASeqData
23 months ago
Maka
• 0
2
votes
3
replies
936
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect
sva
DESeq2
RNASeqData
limma
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
D-Bug
▴ 10
0
votes
3
replies
918
views
Contrasting LogFCs in DESeq2
DESeq2
RNASeqData
updated 2.8 years ago by
swbarnes2
★ 1.3k • written 2.8 years ago by
GlycineMax
• 0
3
votes
3
replies
1.1k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
6 months ago
Ethan Nguyen
• 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
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
0
votes
3
replies
697
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
2
votes
3
replies
698
views
Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 5 months ago by
swbarnes2
★ 1.3k • written 5 months ago by
Sam
• 0
0
votes
3
replies
7.2k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor
RNASeqData
DESeq2
Rsubread
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
Rafael
• 0
1
vote
2
replies
769
views
Pathway analysis of RNAseq data using goseq package
Pathways
goseq
RNASeqData
2.1 years ago • updated 2.0 years ago
m.glymenaki
• 0
0
votes
2
replies
283
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
3 months ago
Luca
• 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
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
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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…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
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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