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limma-voom
•
reset
2
votes
13
replies
2.1k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom
design matrix
limma time-course
limma design matrix
limma
6.2 years ago • updated 6.1 years ago
SPbeginner
• 0
3
votes
14
replies
2.6k
views
limma-voom or edgeR for paired designs both within and between comparisons
edger
limma-voom
paired samples
7.6 years ago
aec
▴ 90
5
votes
2
replies
1.3k
views
voomWithQualityWeights: question on min. number of replicates per group + design to use
limma
edger
voom
voomWithQualityWeights
limma-voom
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
Guido Hooiveld
★ 3.9k
10
votes
5
replies
2.5k
views
limma-voom duplicateCorrelation once or twice, difference?
limma-voom
duplicatecorrelation
random effects
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
tcalvo
▴ 90
3
votes
2
replies
1.2k
views
edgeR QL with voom weights
edger
limma-voom
voom
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
gregory.l.stone
▴ 10
2
votes
3
replies
1.9k
views
Limma voom mechanism
rnaseq
limma
limma-voom
Tutorial
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
icxa0409
• 0
2
votes
15
replies
3.0k
views
limma: how to use pairing and adjust for covariates
limma
limma-voom
limma paired analysis
limma contrast matrix
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
gregory.l.stone
▴ 10
6
votes
4
replies
4.8k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom
limma-voom
tximport
edger
updated 7.1 years ago by
Ryan C. Thompson
★ 7.9k • written 7.1 years ago by
johnmcma
▴ 10
0
votes
7
replies
2.5k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom
sva
duplicatecorrelation
updated 6.8 years ago by
sina.nassiri
▴ 130 • written 6.8 years ago by
aec
▴ 90
1
vote
6
replies
2.4k
views
normalization affects drastically limma-voom + sva results
normalization
sva
limma-voom
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
aec
▴ 90
1
vote
4
replies
1.4k
views
Can I combine quants from SE and PE reads from replicates of same sample in Salmon Quasi-mapping mode?
salmon
tximport
limma-voom
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
Sandip Darji
▴ 30
10
votes
9
replies
1.7k
views
Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
limma-voom
voom
limma
rna-seq
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
vd4mmind
• 0
0
votes
3
replies
1.1k
views
upperquartile with voom
limma-voom
rnaseq
normalization
6.3 years ago
bilcodygm
• 0
0
votes
3
replies
1.2k
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma
limma-voom
goseq
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
joelrosa
• 0
2
votes
1
reply
4.1k
views
voomWithQualityWeights, design and weights
voom
limma-voom
voomwithqualityweights
rna-seq
updated 6.2 years ago by
Matthew Ritchie
▴ 1000 • written 6.3 years ago by
anne.biton
▴ 20
0
votes
3
replies
1.2k
views
quantile normalization takes into account library size?
quantile normalization
limma-voom
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
bilcodygm
• 0
4
votes
4
replies
1.9k
views
Limma-voom with external observation weights
limma
limma-voom
updated 6.1 years ago by
Gordon Smyth
50k • written 6.1 years ago by
Peter Langfelder
★ 3.0k
0
votes
8
replies
2.0k
views
Limma : time course experiment with missing data
limma
limma-voom
updated 12 months ago by
blackdesgin
• 0 • written 6.1 years ago by
SPbeginner
• 0
2
votes
6
replies
1.7k
views
Building a biologically meaningful design matrix for limma/voom in a large RNASeq experiment
limma
limma-voom
limma design matrix
confounders
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
S.Bamopoulos
▴ 10
1
vote
8
replies
1.8k
views
time series, block by patient, between and within comparisons limma-voom
rna-seq
time series
patient
limma-voom
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
aec
▴ 90
0
votes
4
replies
2.0k
views
PCA plot of variance stabilized transformation of normalized counts in limma
limma-voom
deseq2
EdgeR
updated 5.5 years ago by
Steve Lianoglou
★ 13k • written 5.5 years ago by
Raymond
▴ 20
2
votes
4
replies
1.6k
views
Inconsistent result between limma/voom and DESeq2
deseq2
limma
voom
limma-voom
rnaseq
updated 5.4 years ago by
Gordon Smyth
50k • written 5.4 years ago by
bharata1803
▴ 60
1
vote
3
replies
911
views
Limma-voom with inverse probability weights (similar to sample weights)
limma
limma-voom
StatisticalMethod
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
jay
• 0
1
vote
2
replies
636
views
should smooth quantile normalization be used with limma-voom?
limma-voom
smooth-quantile-normalization
quantro
22 months ago
raf4
▴ 20
0
votes
2
replies
1.3k
views
voom flips the sign relative to log(cpm)
limma
limma-voom
rnaseq
voom
updated 2.6 years ago by
Gordon Smyth
50k • written 2.6 years ago by
taur.vil
• 0
3
votes
5
replies
891
views
limma-trend vs. limma-voom theoretical difference
limma
limma-trend
limma-voom
updated 3 months ago by
floriandeckert
▴ 30 • written 17 months ago by
hainct
• 0
0
votes
5
replies
956
views
Semi-technical replicates and voom sample weights
variancePa
variancePartition
limma-voom
dream
updated 14 months ago by
Gordon Smyth
50k • written 14 months ago by
Le
• 0
2
votes
5
replies
1.4k
views
Limma-Voom which of two models is correct?
limma-voom
rnaseq
differential gene expression
7.6 years ago
Javier Gutierrez-Achury
• 0
1
vote
5
replies
1.8k
views
Limma: paired multifactor analysis
limma
limma design matrix
limma contrast matrix
limma paired analysis
limma-voom
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
gregory.l.stone
▴ 10
1
vote
2
replies
1.7k
views
limma contrast with interaction and paired samples
limma
limma-voom
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
gregory.l.stone
▴ 10
0
votes
2
replies
1.2k
views
assess quality of data
rnaseq
edger
limma-voom
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
bilcodygm
• 0
31 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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