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limma voom
•
reset
1
vote
12
replies
3.7k
views
Limma-voom design for multifactorial RNA-seq experiment
limma voom
multiple factor design
limma
voom
8.4 years ago
oliver.selmoni
• 0
7
votes
8
replies
5.3k
views
Limma Voom produces many identical adjusted p-values
limma voom
adjusted pvalue
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
b.nota
▴ 360
4
votes
5
replies
7.2k
views
Limma voom or trend?
limma voom
limma-trend
updated 6.2 years ago by
max.moldovan
• 0 • written 7.3 years ago by
b.nota
▴ 360
5
votes
9
replies
5.9k
views
Voom: need at least two non-NA values to interpolate
limma voom
voom
rsem
fpkm
7.7 years ago • updated 7.6 years ago
komal.rathi
▴ 120
4
votes
3
replies
1.4k
views
Accounting for both categorical and numerical possible confounding variables in the limmaVoom pipeline
limma
limma voom
duplicatecorrelation
6.8 years ago
LR0306
▴ 10
2
votes
4
replies
1.3k
views
limma voom - time course experiment - multi level experiment
limma
duplicatecorrelation
limma voom
6.0 years ago • updated 5.1 years ago
SPbeginner
• 0
24
votes
11
replies
18k
views
when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom
limma
voom
rna-seq
quantile normalization
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
lassancejm
▴ 50
3
votes
5
replies
2.1k
views
Limma-voom contrast confusion
limma
limma voom
limma design matrix
limma contrast matrix
limma paired analysis
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
gregory.l.stone
▴ 10
4
votes
13
replies
1.9k
views
limma and edgeR QL strange results
limma
limma voom
edger
updated 7.2 years ago by
Ryan C. Thompson
★ 7.9k • written 7.2 years ago by
gregory.l.stone
▴ 10
1
vote
6
replies
3.3k
views
Multiple testing limma contrasts
limma
limma voom
limma contrast matrix
multiple testing correction
updated 7.2 years ago by
James W. MacDonald
65k • written 7.2 years ago by
gregory.l.stone
▴ 10
2
votes
11
replies
2.1k
views
Multi-factorial design for patient-replicates from different time points using duplicate correlation LIMMA Voom
limma
limma voom
duplicatecorrelation
7.1 years ago
alva.james
• 0
6
votes
6
replies
4.8k
views
limma blocking and including covariates
limma
limma voom
paired samples
updated 7.1 years ago by
Ryan C. Thompson
★ 7.9k • written 7.1 years ago by
gstone2
• 0
5
votes
3
replies
2.1k
views
Correct contrast for testing multi-level interaction effect in limma using combined factors design matrix
limma contrast matrix
limma design matrix
limma
rna-seq
limma voom
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Jane Park
• 0
1
vote
3
replies
1.7k
views
Three factor model matrix, contrasts with interactions - DESeq2 / edgeR
deseq2
edgeR
multifactorial design
limma voom
updated 7.0 years ago by
Michael Love
41k • written 7.0 years ago by
Alan Smith
▴ 150
1
vote
1
reply
2.1k
views
limma voom's (and edger's) use of scaling factors
limma
limma voom
normalization
edger
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
biominer
▴ 10
1
vote
7
replies
1.9k
views
limma - Multi-level Experiments - time course data
limma
limma voom
rnaseq_analysis
DEG
6.1 years ago • updated 5.1 years ago
SPbeginner
• 0
3
votes
4
replies
2.1k
views
limma-voom WithQualityWeights and duplicateCorrelation in RNA-seq
voomwithqualityweights
limma voom
duplicatecorrelation
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
BharathAnanth
▴ 80
1
vote
6
replies
2.0k
views
Differentially expressed genes across multiple conditions
differential gene expression
limma voom
multiple treatments
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
vam3002
• 0
3
votes
5
replies
1.4k
views
Normalization for small non-coding RNA and multi-factor design
edger
limma voom
normalization
limma
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
Konstantinos Yeles
▴ 80
3
votes
3
replies
1.2k
views
Voom shows error message:
Limma voom
edger
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
mahmudornob
• 0
4
votes
4
replies
1.5k
views
Setting contrasts in limma where null hypothesis is that Test = 2 x Control
differential gene expression
limma
rnaseq
design and contrast matrix
limma voom
8.3 years ago
stuart
▴ 10
3
votes
1
reply
2.6k
views
Clustering with differentially expressed genes in RNAseq
deseq2
limma voom
edger
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
User34591
• 0
3
votes
9
replies
6.2k
views
Limma-voom vs limma-trend
limma
limma voom
limma-trend
updated 7.4 years ago by
Gordon Smyth
50k • written 7.4 years ago by
Nik Tuzov
▴ 80
2
votes
3
replies
3.7k
views
voom on normalised counts
limma voom
rnaseq
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
i.sudbery
▴ 40
2
votes
3
replies
1.6k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
7.3 years ago
Pekka Kohonen
▴ 190
1
vote
2
replies
2.0k
views
How to use 'IHW' package to filter genes?
ihw
deseq2
edger
limma voom
updated 7.3 years ago by
Bernd Klaus
▴ 610 • written 7.3 years ago by
tofukaj
• 0
1
vote
0
replies
1.2k
views
visualizing top differentially spliced genes
limma voom
alternative splicing
8.2 years ago
osa.zuta
▴ 40
27 results • Page
1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons
by
Michael Love
41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result
by
ATpoint
★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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