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Showing :
RNASeqData
•
reset
22
votes
15
replies
7.5k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 6 months ago by
Marie
▴ 10 • written 2.1 years ago by
Dina
▴ 50
8
votes
2
replies
7.0k
views
handling outliers with DESeq2
RNASeqData
DESeq2
Outliers
3.0 years ago
paty
▴ 60
7
votes
5
replies
3.4k
views
Normalise to a housekeeping gene in DESEq2
DESeq2
housekeeping
R
RNASeqData
3.5 years ago • updated 3.4 years ago
ecg1g15
▴ 20
6
votes
4
replies
11k
views
How to use combat in order to remove batch effects?
BatchEffect
DESeq2
RNASeqData
updated 2.3 years ago by
BioNovice247
• 0 • written 3.2 years ago by
Emma
▴ 10
5
votes
6
replies
572
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
3 months ago
Shaimaa Gamal
• 0
4
votes
3
replies
1.2k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2
idep
RNASeqData
updated 2.2 years ago by
swbarnes2
★ 1.4k • written 2.2 years ago by
student2
▴ 10
4
votes
1
reply
2.4k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2
RNASeq
RNASeqData
updated 2.1 years ago by
Michael Love
42k • written 2.1 years ago by
treebig44
▴ 30
3
votes
6
replies
1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2
RNASeqData
DifferentialExpression
updated 3.4 years ago by
Michael Love
42k • written 3.5 years ago by
Ben
▴ 50
3
votes
3
replies
1.4k
views
How to formulate 2 factor nested design in DESeq2
nested_design
RNASeqData
DESeq2
23 months ago
JK Kim
▴ 20
3
votes
2
replies
935
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData
DEGreport
edgeR
3.2 years ago
Wuschel
▴ 10
3
votes
3
replies
947
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
10 months ago
amnahsiddiqa
▴ 10
3
votes
2
replies
680
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod
RNASeqData
edgeR
DESeq2
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
CDSPARKS
▴ 10
3
votes
6
replies
8.8k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2
RNASeq
RNASeqData
2.2 years ago
treebig44
▴ 30
3
votes
4
replies
1.4k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.1 years ago
hgalmoore
• 0
3
votes
4
replies
544
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
3
votes
5
replies
642
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 9 weeks ago by
Michael Love
42k • written 10 weeks ago by
sap275
▴ 10
3
votes
2
replies
952
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
2.1 years ago • updated 2.0 years ago
Dakarai
▴ 10
3
votes
3
replies
1.2k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
7 months ago
Ethan Nguyen
• 0
2
votes
3
replies
1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
amnahsiddiqa
▴ 10
2
votes
2
replies
416
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
5 months ago
Manthos
• 0
2
votes
1
reply
697
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData
DataImport
oligo
RNASeqData
convert
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
rodj5201
• 0
2
votes
4
replies
701
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
7 months ago
Shihui
• 0
2
votes
9
replies
2.3k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
23 months ago • updated 22 months ago
Peipei
• 0
2
votes
4
replies
2.8k
views
Compare 3 RNASeq groups with no control in DESeq2
anova
RNASeqData
tukeyTest
DESeq2
3.5 years ago
ecg1g15
▴ 20
2
votes
3
replies
831
views
Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 6 months ago by
swbarnes2
★ 1.4k • written 6 months ago by
Sam
• 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 23 days ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
2
votes
8
replies
2.3k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.1 years ago by
Gordon Smyth
50k • written 3.1 years ago by
Rishav
▴ 20
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 14 months ago by
Rebekah
• 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport
tx2gene
rnas
DESeq2
RNASeqData
2.0 years ago
Maka
• 0
2
votes
3
replies
1.1k
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 9 months ago by
James W. MacDonald
65k • written 9 months ago by
D-Bug
▴ 10
2
votes
3
replies
1.4k
views
RNA-seq analysis without replicates
DESeq2
RESEQ
RNASeqData
updated 13 months ago by
Cynthia
• 0 • written 13 months ago by
4214811
• 0
2
votes
4
replies
1.2k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData
DESeq2
2.7 years ago
khaveh
▴ 10
1
vote
1
reply
603
views
DESEQ2 differential expression for subsets of data?
RNASeqData
DESeq2
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
amnahsiddiqa
▴ 10
1
vote
1
reply
460
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Sara
• 0
1
vote
7
replies
855
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 5 months ago by
Gordon Smyth
50k • written 7 months ago by
Gimena
• 0
1
vote
1
reply
652
views
Strange error while running DESeq() function.
DESeq2
RNASeq
RNASeqData
updated 2.2 years ago by
Michael Love
42k • written 2.2 years ago by
treebig44
▴ 30
1
vote
1
reply
768
views
NOIseq Probability column
RNAseq
RNASeqData
NOISeq
23 months ago
Pratibha
▴ 10
1
vote
2
replies
680
views
Installation of R-packages for RNA-seq analysis
RNASeqData
14 months ago
Begin-R
• 0
1
vote
1
reply
410
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData
DifferentialExpression
DESeq2
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
kubracelikbas4
• 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 12 months ago by
informatician
• 0
1
vote
1
reply
2.2k
views
Limma interaction term
RNASeqData
limma
DifferentialExpression
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
bageerathan.v
• 0
1
vote
2
replies
680
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
5 months ago • updated 4 months ago
Levi
• 0
1
vote
6
replies
1.4k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData
DESeq2
rnaseqGene
3.2 years ago
Seaweed
• 0
1
vote
2
replies
2.6k
views
Understanding how to contrast two treatments in DESeq2
DESeq2
RNASeqData
updated 20 months ago by
swbarnes2
★ 1.4k • written 20 months ago by
Jennifer M
• 0
1
vote
1
reply
1.2k
views
Help understanding edgeR code for doing exactTest
exacttest
RNASeqData
edgeR
diffGeneAnalysis
updated 2.5 years ago by
Gordon Smyth
50k • written 2.5 years ago by
Julia
• 0
1
vote
1
reply
342
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
kaurprab
• 0
1
vote
4
replies
1.3k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
16 months ago
Iwan
• 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq
RNASeqData
updated 23 months ago by
ATpoint
★ 4.1k • written 23 months ago by
Sanatan
• 0
1
vote
3
replies
1.7k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
3.1 years ago
dantasezequiel1
• 0
1
vote
2
replies
830
views
Pathway analysis of RNAseq data using goseq package
Pathways
goseq
RNASeqData
2.2 years ago • updated 2.1 years ago
m.glymenaki
• 0
50 results • Page
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Replies
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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