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RnaSeq
•
reset
52
votes
20
replies
44k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 7.9 years ago by
adam
• 0 • written 8.4 years ago by
AB
▴ 110
17
votes
14
replies
40k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 22 months ago by
OE
• 0 • written 6.8 years ago by
cms72
▴ 20
19
votes
6
replies
35k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq
annotationdbi
updated 7.6 years ago by
Valerie Obenchain
★ 6.8k • written 7.6 years ago by
gokce.ouz
▴ 70
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger
rnaseq
differential expression
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
Pauly Lin
▴ 150
22
votes
13
replies
26k
views
gene dispersion, what does it mean?
gener
rnaseq
updated 13 months ago by
Gordon Smyth
50k • written 8.4 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 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
bmreilly
• 0
1
vote
19
replies
25k
views
Import bamfiles for RNAsequencing analysis
R
rnaseq
bam file
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
Merlin
▴ 10
8
votes
10
replies
25k
views
Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
9.0 years ago
AurelieMLB
▴ 50
4
votes
3
replies
22k
views
Fisher test in Rna seq
rna-seq
rnaseq
r
updated 4.8 years ago by
Gordon Smyth
50k • written 5.4 years ago by
g.k
• 0
9
votes
8
replies
21k
views
Integrating DESeq2 and TopGO for Enrichment
go
deseq2
rnaseq
r
updated 9.2 years ago by
Bernd Klaus
▴ 610 • written 9.2 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
7.0 years ago
zeynep.nenseth
• 0
3
votes
6
replies
20k
views
DESeq2: QQ plot of P-values
deseq2
rnaseq
rna-seq
6.8 years ago
nikmehr22
• 0
32
votes
16
replies
18k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 6.0 years ago by
luxeredias
▴ 20 • written 7.8 years ago by
tangming2005
▴ 190
6
votes
12
replies
17k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2
deseq
counts
rnaseq
differential gene expression
updated 8.0 years ago by
Michael Love
41k • written 8.0 years ago by
wannes.nauwynck
▴ 10
0
votes
4
replies
16k
views
3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2
rnaseq
PCA
updated 9.1 years ago by
Michael Love
41k • written 9.1 years ago by
erin.gill81
▴ 60
21
votes
13
replies
16k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger
rnaseq
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
candida.vaz
▴ 50
3
votes
2
replies
16k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq
edgeR
rpkm
updated 12 months ago by
Gordon Smyth
50k • written 10.0 years ago by
shirley zhang
★ 1.0k
11
votes
1
reply
16k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq
deseq2
updated 8.5 years ago by
Michael Love
41k • written 8.5 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 7.5 years ago by
Simon Anders
★ 3.7k • written 7.5 years ago by
mbeckste
▴ 30
1
vote
13
replies
14k
views
Count matrix from Kallisto as input for DESeq2
rnaseq
deseq2
kallisto
7.7 years ago
yjliu1127
• 0
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
7
votes
8
replies
13k
views
DESeq2: one condition vs multiple combined
rnaseq
deseq2
updated 6.1 years ago by
rammohanshukla
▴ 10 • written 7.7 years ago by
Konstantin Okonechnikov
▴ 40
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 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
ricardo3889
• 0
1
vote
1
reply
12k
views
Deseq2 for RNAseq experiments without replicates
rnaseq
deseq2
updated 8.3 years ago by
Michael Love
41k • written 8.3 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 8.3 years ago by
Michael Love
41k • written 8.3 years ago by
Bstn132
• 0
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 12 months ago by
ATpoint
★ 4.1k • written 7.8 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 6.8 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 7.3 years ago by
Gordon Smyth
50k • written 7.3 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
8.6 years ago
nickbern92
• 0
6
votes
6
replies
11k
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
6.5 years ago
Jack
• 0
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2
rnaseq
statistics
updated 7 months ago by
camillab.
▴ 10 • written 6.6 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 8.5 years ago by
Jeff Leek
▴ 650 • written 8.5 years ago by
AB
▴ 110
9
votes
6
replies
10k
views
Error bars DESeq or DESeq2 fold change
rnaseq
deseq2
deseq
standard error
confidence interval
updated 2.5 years ago by
Michael Love
41k • written 8.1 years ago by
lisa.crossman
▴ 10
3
votes
11
replies
10k
views
How to interpret plotBCV plots in edgeR
rnaseq
edger
7.2 years ago
davide.bau
• 0
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 3 months ago by
Shaimaa Gamal
• 0 • written 7.1 years ago by
myprogramming2016
• 0
1
vote
6
replies
9.9k
views
Change fontsize/remove name of annotation ComplexHeatmap package
r
rnaseq
complexHeatmap
annotation
updated 3.9 years ago by
Zuguang Gu
▴ 260 • written 3.9 years ago by
camillab.
▴ 10
2
votes
5
replies
9.9k
views
DESeq2 Following RSEM
deseq2
rnaseq
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
tungphannv
▴ 10
1
vote
1
reply
9.8k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq
deseq2
r
updated 9.2 years ago by
Ryan C. Thompson
★ 7.9k • written 9.2 years ago by
nw328
▴ 20
21
votes
7
replies
9.6k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
Jack
• 0
8
votes
11
replies
9.4k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
updated 7.8 years ago by
David ROUX
▴ 20 • written 7.9 years ago by
alireza_sharifian_10
▴ 10
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 6 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
2
votes
6
replies
9.0k
views
Estimation of dispersion in DeSeq and DeSeq2
deseq
deseq2
rnaseq
updated 9.4 years ago by
Michael Love
41k • written 9.4 years ago by
JK
▴ 10
3
votes
9
replies
9.0k
views
merge fastq.gz in R? (or in Windows?)
rnaseq
bioconductor
fastq
updated 3.4 years ago by
Rafael
• 0 • written 8.8 years ago by
mk.applebee
• 0
1
vote
6
replies
8.9k
views
Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
rnaseq
r
biomart
updated 8.5 years ago by
Johannes Rainer
★ 2.0k • written 8.5 years ago by
kmuench
▴ 40
3
votes
6
replies
8.8k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2
RNASeq
RNASeqData
2.1 years ago
treebig44
▴ 30
4
votes
14
replies
8.8k
views
Extracting custom post-normalization counts from DESeq2
deseq2
r
ruvseq
normalization
rnaseq
8.8 years ago
nickp60
• 0
7
votes
7
replies
8.7k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2
LRT
rnaseq
design
reduced model
updated 5.4 years ago by
evocanres
• 0 • written 7.0 years ago by
I.Castanho
▴ 50
3
votes
5
replies
8.5k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 9.5 years ago by
Steve Lianoglou
★ 13k • written 9.5 years ago by
Peter Crisp
▴ 10
3
votes
4
replies
8.2k
views
DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative integer"
DESeqDataSet
DESeqDataSetFromMatrix
rnaseq
deseq2
7.8 years ago
ErickF
▴ 40
6
votes
6
replies
8.1k
views
EdgeR design matrix with 3 factors
edger
glm
rnaseq
6.4 years ago
Denniswu
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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