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RNAseq
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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
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
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
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
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
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
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
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
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
18
votes
17
replies
3.9k
views
How to model a comparison between comparisons in edgeR?
edger
rnaseq
updated 9.1 years ago by
Ryan C. Thompson
★ 7.9k • written 9.1 years ago by
Nick N
▴ 60
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
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
15
votes
4
replies
2.7k
views
Using multiple tools for differential gene expression analysis as validation
edger
limma
deseq2
rnaseq
updated 7.8 years ago by
Ryan C. Thompson
★ 7.9k • written 7.8 years ago by
WouterDeCoster
▴ 130
15
votes
3
replies
1.5k
views
lfcShrink function for different comparison
DESeq2
RNASeq
updated 2.1 years ago by
molly_the_minotaur
▴ 30 • written 3.4 years ago by
bi.mi
▴ 90
13
votes
5
replies
6.9k
views
EDGE-R exact test vs QL F-test
edger
rnaseq
updated 23 months ago by
Sarah
• 0 • written 7.8 years ago by
kaihami
▴ 30
12
votes
6
replies
3.3k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq
deseq2
edger
8.3 years ago
martiningi
▴ 40
12
votes
12
replies
2.0k
views
FDR does not change between genes in edgeR
RNAseq
edgeR
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
apfelbapfel
▴ 30
12
votes
13
replies
7.6k
views
EdgeR Differential Expression analysis with NAs
EdgeR
rnaseq
NA
updated 9.5 years ago by
Aaron Lun
★ 28k • written 9.5 years ago by
elliott77
• 0
12
votes
6
replies
2.5k
views
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger
differential gene expression
rnaseq
updated 7.0 years ago by
Gordon Smyth
50k • written 7.0 years ago by
gabriel.rosser
▴ 20
11
votes
7
replies
6.2k
views
What's the rationale for using the negative binomial distribution to model read counts?
rnaseq
updated 7.7 years ago by
Ryan C. Thompson
★ 7.9k • written 7.7 years ago by
kjo
▴ 70
11
votes
14
replies
4.2k
views
Setting up the Design Matrix
rnaseq
edgeR
multiple factor design
design matrix
8.2 years ago
Yogender Gowtham
▴ 20
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
11
votes
11
replies
3.3k
views
Different results in edgeR using simple vs GLM
edger
glm
rnaseq
8.5 years ago • updated 8.4 years ago
dietahanson
▴ 30
11
votes
0
replies
5.7k
views
Tutorial:
Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges
Annotation
RNAseq
visualization
Tutorial
8.7 years ago
Martin Morgan
25k
11
votes
9
replies
4.3k
views
How to remove more than two batches in my data-sets
limma
RNAseq
removebatcheffect()
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 years ago by
yi.huang
▴ 30
10
votes
6
replies
4.6k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq
deseq2
edger
voom
limma
updated 6.5 years ago by
Paul Harrison
▴ 100 • written 8.8 years ago by
Sean Davis
21k
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
10
votes
10
replies
6.9k
views
GLM Likelihood ratio test
rnaseq
edgeR
GLM
updated 9.1 years ago by
Gordon Smyth
50k • written 9.1 years ago by
ygowtha
• 0
10
votes
8
replies
2.8k
views
Best alternative annotation package to BiomaRt
R
biomaRt
Ensembl
rnaseq
4.7 years ago
m93
▴ 10
9
votes
3
replies
4.5k
views
Limma vs deseq2 results
limma
RNASeq
R
22 months ago
k___
▴ 30
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
9
votes
6
replies
1.8k
views
Representative gene expression value in one condition with several replicates
rnaseq
gene expression
edger
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
Jack
• 0
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
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
9
votes
4
replies
3.3k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon
cqn
tximport
deseq2
rnaseq
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
dmr210
▴ 30
9
votes
9
replies
5.2k
views
Voom on TCGA data shifts count distributions towards negative values
voom
TCGA
RNAseq
9.3 years ago
paola.ostano
▴ 10
8
votes
0
replies
3.5k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
8.8 years ago
Martin Morgan
25k
8
votes
3
replies
1.8k
views
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
edgeR
rnaseq
limma
independent filtering
6.5 years ago
Robert Castelo
★ 3.1k
8
votes
11
replies
6.3k
views
[DESeq2] Cook's distance flagging for continuous variables
deseq2
rnaseq
updated 8.8 years ago by
Michael Love
41k • written 8.8 years ago by
enricoferrero
▴ 660
8
votes
11
replies
1.2k
views
Is there any model in EdgeR that is close to nested ANOVA?
edger
rnaseq
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
deeptiptl74
▴ 10
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
8
votes
10
replies
25k
views
Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
8.9 years ago
AurelieMLB
▴ 50
8
votes
8
replies
4.0k
views
Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell data
rnaseq
single cell
normalization
edgeR
deseq2
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
kieranrcampbell
▴ 50
8
votes
4
replies
2.5k
views
edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
hemoglobin
edgeR
deseq2
normalization
rnaseq
updated 5.1 years ago by
Ryan C. Thompson
★ 7.9k • written 5.1 years ago by
aec
▴ 90
8
votes
3
replies
2.9k
views
Testing three-way interactions in DESeq2
deseq2
rna-seq
rnaseq
interactions
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
red_bricks
▴ 50
8
votes
3
replies
1.4k
views
Counting ambiguously mapped reads per feature
rnaseq
bam
genomicranges
GenomicAlignments
Rsamtools
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 years ago by
rubi
▴ 110
8
votes
7
replies
1.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq
edger
differential gene expression
batch effect
updated 4.8 years ago by
Victoria
• 0 • written 5.5 years ago by
Laura
▴ 20
8
votes
4
replies
1.6k
views
Equivalence tests with edgeR
rnaseq
edger
equivalence
updated 9.0 years ago by
Aaron Lun
★ 28k • written 9.0 years ago by
roberto.spreafico
▴ 20
8
votes
8
replies
6.6k
views
Voom transformation from counts and normalization to negative values
rnaseq
voom
limma
tcga
statistics
updated 5.5 years ago by
Ryan C. Thompson
★ 7.9k • written 5.5 years ago by
Beginner
▴ 60
7
votes
4
replies
2.4k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count
rnaseq
rpkm
fpkm
edgeR
updated 9.0 years ago by
Gordon Smyth
50k • written 9.0 years ago by
thibault.lorin
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Answer: Minfi - estimatecellscount
by
James W. MacDonald
65k
Don't filter first. You are likely removing the CpGs that are used to estimate the cell counts.
Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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