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rnaseq
•
reset
52
votes
20
replies
43k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 7.8 years ago by
adam
• 0 • written 8.3 years ago by
AB
▴ 110
17
votes
14
replies
39k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 21 months ago by
OE
• 0 • written 6.7 years ago by
cms72
▴ 20
19
votes
6
replies
34k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq
annotationdbi
updated 7.5 years ago by
Valerie Obenchain
★ 6.8k • written 7.5 years ago by
gokce.ouz
▴ 70
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger
rnaseq
differential expression
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
Pauly Lin
▴ 150
22
votes
13
replies
26k
views
gene dispersion, what does it mean?
gener
rnaseq
updated 12 months ago by
Gordon Smyth
50k • written 8.3 years ago by
tonja.r
▴ 80
3
votes
7
replies
26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
bmreilly
• 0
8
votes
10
replies
25k
views
Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
8.9 years ago
AurelieMLB
▴ 50
1
vote
19
replies
25k
views
Import bamfiles for RNAsequencing analysis
R
rnaseq
bam file
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
Merlin
▴ 10
4
votes
3
replies
22k
views
Fisher test in Rna seq
rna-seq
rnaseq
r
updated 4.7 years ago by
Gordon Smyth
50k • written 5.3 years ago by
g.k
• 0
9
votes
8
replies
21k
views
Integrating DESeq2 and TopGO for Enrichment
go
deseq2
rnaseq
r
updated 9.1 years ago by
Bernd Klaus
▴ 610 • written 9.1 years ago by
nw328
▴ 20
0
votes
4
replies
21k
views
DESeq2: How do I compare certain samples that are in two groups and two treatments
deseq2
rnaseq
R
6.9 years ago
zeynep.nenseth
• 0
3
votes
6
replies
20k
views
DESeq2: QQ plot of P-values
deseq2
rnaseq
rna-seq
6.7 years ago
nikmehr22
• 0
32
votes
16
replies
17k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 5.9 years ago by
luxeredias
▴ 20 • written 7.7 years ago by
tangming2005
▴ 190
6
votes
12
replies
16k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2
deseq
counts
rnaseq
differential gene expression
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
wannes.nauwynck
▴ 10
21
votes
13
replies
16k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger
rnaseq
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
candida.vaz
▴ 50
0
votes
4
replies
16k
views
3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2
rnaseq
PCA
updated 9.0 years ago by
Michael Love
41k • written 9.0 years ago by
erin.gill81
▴ 60
3
votes
2
replies
16k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq
edgeR
rpkm
updated 11 months ago by
Gordon Smyth
50k • written 9.9 years ago by
shirley zhang
★ 1.0k
11
votes
1
reply
15k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq
deseq2
updated 8.4 years ago by
Michael Love
41k • written 8.4 years ago by
tony_cybercloud
▴ 20
25
votes
7
replies
14k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq
deseq2
ercc
updated 7.4 years ago by
Simon Anders
★ 3.7k • written 7.4 years ago by
mbeckste
▴ 30
1
vote
13
replies
13k
views
Count matrix from Kallisto as input for DESeq2
rnaseq
deseq2
kallisto
7.6 years ago
yjliu1127
• 0
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 21 months ago by
Mohamed
▴ 30
7
votes
8
replies
12k
views
DESeq2: one condition vs multiple combined
rnaseq
deseq2
updated 6.0 years ago by
rammohanshukla
▴ 10 • written 7.6 years ago by
Konstantin Okonechnikov
▴ 40
1
vote
1
reply
12k
views
Deseq2 for RNAseq experiments without replicates
rnaseq
deseq2
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
prp291
• 0
6
votes
2
replies
12k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2
R
rnaseq
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
Bstn132
• 0
0
votes
8
replies
12k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
ricardo3889
• 0
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 11 months ago by
ATpoint
★ 4.0k • written 7.7 years ago by
EJ
▴ 20
9
votes
7
replies
11k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2
rnaseq
pca
tsne
updated 6.7 years ago by
Kushal K Dey
▴ 10 • written 6.8 years ago by
s.w.vanderlaan
▴ 30
25
votes
37
replies
11k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq
RSEM
TCGA
edgeR
normalization
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
svlachavas
▴ 830
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq
normalization
tpm
tmm
8.5 years ago
nickbern92
• 0
6
votes
6
replies
10k
views
Why different filtering criteria using CPM to filter the RNA-seq count data in edgeR have so much influence on the number of DE genes?
rnaseq
edger
6.4 years ago
Jack
• 0
25
votes
7
replies
10k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2
rnaseq
statistics
updated 5 months ago by
camillab.
▴ 10 • written 6.5 years ago by
Russ Fraser
▴ 30
10
votes
6
replies
10k
views
Estimating and removing batch effects from rna-seq dataset
sva
batch effect
rnaseq
removebatcheffect()
limma
updated 8.4 years ago by
Jeff Leek
▴ 650 • written 8.4 years ago by
AB
▴ 110
9
votes
6
replies
9.9k
views
Error bars DESeq or DESeq2 fold change
rnaseq
deseq2
deseq
standard error
confidence interval
updated 2.4 years ago by
Michael Love
41k • written 8.0 years ago by
lisa.crossman
▴ 10
3
votes
11
replies
9.9k
views
How to interpret plotBCV plots in edgeR
rnaseq
edger
7.1 years ago
davide.bau
• 0
5
votes
7
replies
9.9k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 10 weeks ago by
Shaimaa Gamal
• 0 • written 7.0 years ago by
myprogramming2016
• 0
1
vote
1
reply
9.8k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq
deseq2
r
updated 9.1 years ago by
Ryan C. Thompson
★ 7.9k • written 9.1 years ago by
nw328
▴ 20
2
votes
5
replies
9.7k
views
DESeq2 Following RSEM
deseq2
rnaseq
updated 7.0 years ago by
Michael Love
41k • written 7.0 years ago by
tungphannv
▴ 10
1
vote
6
replies
9.6k
views
Change fontsize/remove name of annotation ComplexHeatmap package
r
rnaseq
complexHeatmap
annotation
updated 3.8 years ago by
Zuguang Gu
▴ 240 • written 3.8 years ago by
camillab.
▴ 10
21
votes
7
replies
9.3k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 years ago by
Jack
• 0
8
votes
11
replies
9.3k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
updated 7.7 years ago by
David ROUX
▴ 20 • written 7.8 years ago by
alireza_sharifian_10
▴ 10
0
votes
5
replies
9.1k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 9 days ago by
Eva
• 0 • written 7.5 years ago by
ctl
• 0
2
votes
6
replies
8.9k
views
Estimation of dispersion in DeSeq and DeSeq2
deseq
deseq2
rnaseq
updated 9.3 years ago by
Michael Love
41k • written 9.3 years ago by
JK
▴ 10
1
vote
6
replies
8.8k
views
Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
rnaseq
r
biomart
updated 8.4 years ago by
Johannes Rainer
★ 2.0k • written 8.4 years ago by
kmuench
▴ 40
3
votes
9
replies
8.8k
views
merge fastq.gz in R? (or in Windows?)
rnaseq
bioconductor
fastq
updated 3.3 years ago by
Rafael
• 0 • written 8.7 years ago by
mk.applebee
• 0
4
votes
14
replies
8.7k
views
Extracting custom post-normalization counts from DESeq2
deseq2
r
ruvseq
normalization
rnaseq
8.7 years ago
nickp60
• 0
7
votes
7
replies
8.6k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2
LRT
rnaseq
design
reduced model
updated 5.3 years ago by
evocanres
• 0 • written 6.9 years ago by
I.Castanho
▴ 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
3
votes
5
replies
8.4k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 9.4 years ago by
Steve Lianoglou
★ 13k • written 9.4 years ago by
Peter Crisp
▴ 10
3
votes
4
replies
8.1k
views
DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative integer"
DESeqDataSet
DESeqDataSetFromMatrix
rnaseq
deseq2
7.7 years ago
ErickF
▴ 40
6
votes
6
replies
8.0k
views
EdgeR design matrix with 3 factors
edger
glm
rnaseq
6.3 years ago
Denniswu
▴ 20
50 results • Page
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Comment: error when using M-values in ChAMP
by
hortenseguillaume96
• 0
Hello Tian, I'd like to get the M-values matrix so that I can carry out a linear regression study. However, when I apply the champ.load fu…
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
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
Answer: error in ChAMP loading file
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