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RNASeq
•
reset
52
votes
20
replies
44k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 8.0 years ago by
adam
• 0 • written 8.4 years ago by
AB
▴ 110
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 6.1 years ago by
luxeredias
▴ 20 • written 7.9 years ago by
tangming2005
▴ 190
25
votes
7
replies
15k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq
deseq2
ercc
updated 7.6 years ago by
Simon Anders
★ 3.7k • written 7.6 years ago by
mbeckste
▴ 30
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
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 7.4 years ago by
Gordon Smyth
50k • written 7.4 years ago by
svlachavas
▴ 830
22
votes
13
replies
26k
views
gene dispersion, what does it mean?
gener
rnaseq
updated 14 months ago by
Gordon Smyth
50k • written 8.5 years ago by
tonja.r
▴ 80
22
votes
7
replies
9.7k
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
21
votes
13
replies
16k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger
rnaseq
updated 9.6 years ago by
James W. MacDonald
65k • written 9.6 years ago by
candida.vaz
▴ 50
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 7.7 years ago by
gokce.ouz
▴ 70
18
votes
17
replies
4.1k
views
How to model a comparison between comparisons in edgeR?
edger
rnaseq
updated 9.2 years ago by
Ryan C. Thompson
★ 7.9k • written 9.2 years ago by
Nick N
▴ 60
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 23 months ago by
OE
• 0 • written 6.8 years ago by
cms72
▴ 20
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger
rnaseq
differential expression
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Pauly Lin
▴ 150
15
votes
4
replies
2.8k
views
Using multiple tools for differential gene expression analysis as validation
edger
limma
deseq2
rnaseq
updated 7.9 years ago by
Ryan C. Thompson
★ 7.9k • written 7.9 years ago by
WouterDeCoster
▴ 130
15
votes
3
replies
1.6k
views
lfcShrink function for different comparison
DESeq2
RNASeq
updated 2.3 years ago by
molly_the_minotaur
▴ 30 • written 3.5 years ago by
bi.mi
▴ 90
13
votes
5
replies
7.1k
views
EDGE-R exact test vs QL F-test
edger
rnaseq
updated 2.1 years ago by
Sarah
• 0 • written 7.9 years ago by
kaihami
▴ 30
12
votes
12
replies
2.1k
views
FDR does not change between genes in edgeR
RNAseq
edgeR
updated 5.4 years ago by
Gordon Smyth
50k • written 5.4 years ago by
apfelbapfel
▴ 30
12
votes
13
replies
7.8k
views
EdgeR Differential Expression analysis with NAs
EdgeR
rnaseq
NA
updated 9.7 years ago by
Aaron Lun
★ 28k • written 9.7 years ago by
elliott77
• 0
12
votes
6
replies
3.4k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq
deseq2
edger
8.5 years ago
martiningi
▴ 40
12
votes
6
replies
2.6k
views
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger
differential gene expression
rnaseq
updated 7.1 years ago by
Gordon Smyth
50k • written 7.1 years ago by
gabriel.rosser
▴ 20
11
votes
7
replies
6.4k
views
What's the rationale for using the negative binomial distribution to model read counts?
rnaseq
updated 7.9 years ago by
Ryan C. Thompson
★ 7.9k • written 7.9 years ago by
kjo
▴ 70
11
votes
14
replies
4.3k
views
Setting up the Design Matrix
rnaseq
edgeR
multiple factor design
design matrix
8.3 years ago
Yogender Gowtham
▴ 20
11
votes
1
reply
16k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq
deseq2
updated 8.5 years ago by
Michael Love
42k • written 8.5 years ago by
tony_cybercloud
▴ 20
11
votes
0
replies
5.8k
views
Tutorial:
Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges
Annotation
RNAseq
visualization
Tutorial
8.9 years ago
Martin Morgan
25k
11
votes
11
replies
3.3k
views
Different results in edgeR using simple vs GLM
edger
glm
rnaseq
8.6 years ago
dietahanson
▴ 30
11
votes
9
replies
4.4k
views
How to remove more than two batches in my data-sets
limma
RNAseq
removebatcheffect()
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
yi.huang
▴ 30
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
10
votes
6
replies
4.7k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq
deseq2
edger
voom
limma
updated 6.7 years ago by
Paul Harrison
▴ 100 • written 9.0 years ago by
Sean Davis
21k
10
votes
8
replies
3.0k
views
Best alternative annotation package to BiomaRt
R
biomaRt
Ensembl
rnaseq
4.9 years ago
m93
▴ 10
10
votes
6
replies
10k
views
Estimating and removing batch effects from rna-seq dataset
sva
batch effect
rnaseq
removebatcheffect()
limma
updated 8.6 years ago by
Jeff Leek
▴ 650 • written 8.6 years ago by
AB
▴ 110
10
votes
10
replies
7.0k
views
GLM Likelihood ratio test
rnaseq
edgeR
GLM
updated 9.2 years ago by
Gordon Smyth
50k • written 9.2 years ago by
ygowtha
• 0
9
votes
7
replies
11k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2
rnaseq
pca
tsne
updated 6.9 years ago by
Kushal K Dey
▴ 10 • written 6.9 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 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
Jack
• 0
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
42k • written 8.1 years ago by
lisa.crossman
▴ 10
9
votes
8
replies
21k
views
Integrating DESeq2 and TopGO for Enrichment
go
deseq2
rnaseq
r
updated 9.3 years ago by
Bernd Klaus
▴ 610 • written 9.3 years ago by
nw328
▴ 20
9
votes
4
replies
3.4k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon
cqn
tximport
deseq2
rnaseq
updated 7.2 years ago by
Michael Love
42k • written 7.2 years ago by
dmr210
▴ 30
9
votes
9
replies
5.3k
views
Voom on TCGA data shifts count distributions towards negative values
voom
TCGA
RNAseq
9.5 years ago
paola.ostano
▴ 10
9
votes
3
replies
5.0k
views
Limma vs deseq2 results
limma
RNASeq
R
23 months ago
k___
▴ 30
8
votes
0
replies
3.6k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
8.9 years ago
Martin Morgan
25k
8
votes
3
replies
1.9k
views
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
edgeR
rnaseq
limma
independent filtering
6.7 years ago
Robert Castelo
★ 3.3k
8
votes
11
replies
6.4k
views
[DESeq2] Cook's distance flagging for continuous variables
deseq2
rnaseq
updated 9.0 years ago by
Michael Love
42k • written 9.0 years ago by
enricoferrero
▴ 660
8
votes
11
replies
1.3k
views
Is there any model in EdgeR that is close to nested ANOVA?
edger
rnaseq
updated 3.8 years ago by
Gordon Smyth
50k • written 3.8 years ago by
deeptiptl74
▴ 10
8
votes
11
replies
9.4k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
updated 7.9 years ago by
David ROUX
▴ 20 • written 8.0 years ago by
alireza_sharifian_10
▴ 10
8
votes
10
replies
25k
views
Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
9.0 years ago
AurelieMLB
▴ 50
8
votes
8
replies
4.1k
views
Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell data
rnaseq
single cell
normalization
edgeR
deseq2
updated 7.7 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
kieranrcampbell
▴ 50
8
votes
8
replies
6.8k
views
Voom transformation from counts and normalization to negative values
rnaseq
voom
limma
tcga
statistics
updated 5.7 years ago by
Ryan C. Thompson
★ 7.9k • written 5.7 years ago by
Beginner
▴ 60
8
votes
3
replies
1.5k
views
Counting ambiguously mapped reads per feature
rnaseq
bam
genomicranges
GenomicAlignments
Rsamtools
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
rubi
▴ 110
8
votes
3
replies
3.0k
views
Testing three-way interactions in DESeq2
deseq2
rna-seq
rnaseq
interactions
updated 6.6 years ago by
Michael Love
42k • written 6.6 years ago by
red_bricks
▴ 50
8
votes
4
replies
1.6k
views
Equivalence tests with edgeR
rnaseq
edger
equivalence
updated 9.1 years ago by
Aaron Lun
★ 28k • written 9.1 years ago by
roberto.spreafico
▴ 20
8
votes
7
replies
1.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq
edger
differential gene expression
batch effect
updated 4.9 years ago by
Victoria
• 0 • written 5.7 years ago by
Laura
▴ 20
8
votes
4
replies
2.5k
views
edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
hemoglobin
edgeR
deseq2
normalization
rnaseq
updated 5.3 years ago by
Ryan C. Thompson
★ 7.9k • written 5.3 years ago by
aec
▴ 90
50 results • Page
1 of 1
Recent ...
Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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