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Showing :
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
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 5.2 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
2.2k
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
42k • 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 5.2 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 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 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
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 1 day ago by
Chris
• 0 • written 7.4 years ago by
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: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go! And for comparisons between the cohorts I presume duplicateCorrelation with standar…
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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