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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
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
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
5
votes
6
replies
478
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
9 weeks ago
Shaimaa Gamal
• 0
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
4
votes
1
reply
2.3k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2
RNASeq
RNASeqData
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
treebig44
▴ 30
3
votes
2
replies
631
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod
RNASeqData
edgeR
DESeq2
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
CDSPARKS
▴ 10
3
votes
2
replies
894
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData
DEGreport
edgeR
3.1 years ago
Wuschel
▴ 10
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.0 years ago
hgalmoore
• 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
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
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
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
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
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
2
replies
891
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
24 months ago • updated 23 months ago
Dakarai
▴ 10
2
votes
1
reply
615
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData
DataImport
oligo
RNASeqData
convert
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
rodj5201
• 0
2
votes
2
replies
354
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
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
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
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
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
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
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
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
2
votes
3
replies
1.1k
views
Problem with tximport IDs
tximport
tx2gene
rnas
DESeq2
RNASeqData
23 months ago
Maka
• 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
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
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
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
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
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
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
357
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData
DifferentialExpression
DESeq2
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
kubracelikbas4
• 0
1
vote
1
reply
426
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Sara
• 0
1
vote
1
reply
613
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
1
vote
2
replies
615
views
Installation of R-packages for RNA-seq analysis
RNASeqData
13 months ago
Begin-R
• 0
1
vote
1
reply
721
views
NOIseq Probability column
RNAseq
RNASeqData
NOISeq
22 months ago • updated 21 months ago
Pratibha
▴ 10
1
vote
7
replies
741
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
1
reply
2.0k
views
Limma interaction term
RNASeqData
limma
DifferentialExpression
updated 2.0 years ago by
Gordon Smyth
50k • written 2.1 years ago by
bageerathan.v
• 0
1
vote
2
replies
582
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
3 months ago
Levi
• 0
1
vote
6
replies
1.3k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData
DESeq2
rnaseqGene
3.1 years ago
Seaweed
• 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
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
4
replies
1.2k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
14 months ago
Iwan
• 0
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
1
vote
5
replies
314
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
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
50 results • Page
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Replies
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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