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limma
•
reset
32
votes
0
replies
38k
views
limma moderated t-statistics and B-statistics
Microarray
limma
19.7 years ago • updated 3.6 years ago
Gordon Smyth
50k
32
votes
10
replies
38k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
updated 13 months ago by
manuelsokolov
• 0 • written 10.5 years ago by
Jon Bråte
▴ 250
28
votes
8
replies
12k
views
Removing continuous covariate effects in limma analysis
limma
microarray
updated 6.7 years ago by
Gordon Smyth
50k • written 9.1 years ago by
Pauly Lin
▴ 150
25
votes
9
replies
6.9k
views
voom for spectral counts
limma
voom
proteomics
spectral counts
massspectrometry
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
Ben Neely
▴ 40
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
24
votes
12
replies
12k
views
Nanostring analysis with limma
nanostring
limma
updated 9.0 years ago by
ker61
▴ 20 • written 9.1 years ago by
mali salmon
▴ 370
22
votes
8
replies
4.2k
views
Limma camera function never gives any differentially expressed gene sets
limma
updated 6.8 years ago by
misterrandyclark
• 0 • written 8.8 years ago by
chris86
▴ 420
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
22
votes
4
replies
10.0k
views
Correct assumptions of using limma moderated t-test
limma
statistical inference
variance test
bioconductor
updated 9.0 years ago by
Gordon Smyth
50k • written 9.0 years ago by
svlachavas
▴ 830
21
votes
5
replies
15k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma
voom
updated 9.0 years ago by
Gordon Smyth
50k • written 10.0 years ago by
John Blischak
▴ 190
19
votes
10
replies
4.2k
views
Do the outputs of Limma's competitive gene set methods (camera, romer) require a mutliple testing correction?
limma
romer
updated 8.7 years ago by
Gordon Smyth
50k • written 8.7 years ago by
Jon Manning
▴ 40
18
votes
3
replies
2.9k
views
cameraPR vs geneSetTest and ROAST/CAMERA in general
limma
voomwithqualityweights
gene set analysis
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
BharathAnanth
▴ 80
18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
9.0 years ago • updated 8.8 years ago
svlachavas
▴ 830
18
votes
18
replies
4.8k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma
batch effect
ComBat
differential gene expression
updated 8.6 years ago by
W. Evan Johnson
▴ 850 • written 8.6 years ago by
svlachavas
▴ 830
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
5
replies
4.9k
views
limma voom Mean-variance trend plot: x-axis?
limma
5.1 years ago
AS
▴ 70
17
votes
7
replies
6.0k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 8.0 years ago by
Ryan C. Thompson
★ 7.9k • written 8.0 years ago by
ompandey
▴ 10
16
votes
5
replies
7.5k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma
voom
deseq
normalization
ercc
updated 8.5 years ago by
Gordon Smyth
50k • written 8.5 years ago by
komal.rathi
▴ 120
16
votes
6
replies
3.3k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR
limma
diffSplice
DEXSeq
updated 7.8 years ago by
Charity Law
▴ 90 • written 7.8 years ago by
maltethodberg
▴ 180
16
votes
13
replies
4.4k
views
Camera and ROAST
limma
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 years ago by
Nuno Pires
▴ 30
16
votes
0
replies
3.8k
views
simultaneous use of robust and weighting methods in limma
limma
robust
arrayWeights
10.4 years ago • updated 8.0 years ago
Gordon Smyth
50k
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 18 days ago
Chris
▴ 10
15
votes
14
replies
3.6k
views
extract similar expressed genes (SEGs) rather than DEGs
limma
microarray
updated 9.3 years ago by
Sean Davis
21k • written 9.3 years ago by
Andreas Heider
▴ 340
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
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
28 days ago • updated 17 days ago
Chris
▴ 10
14
votes
16
replies
2.6k
views
Limma - discrepancy in number of significant genes
limma
differential gene expression
microarray
linear model
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
bcbio_uk
▴ 10
14
votes
9
replies
3.8k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma
rna-seq
removebatcheffect()
updated 6.3 years ago by
alakatos
▴ 130 • written 8.1 years ago by
Ekarl2
▴ 80
14
votes
16
replies
2.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma
toptable
8.0 years ago • updated 7.9 years ago
giroudpaul
▴ 40
14
votes
12
replies
9.4k
views
limma lmFit coefficients and p-values
limma
methylation
ewas
updated 7.8 years ago by
Steve Lianoglou
★ 13k • written 7.8 years ago by
CPR
▴ 30
13
votes
2
replies
3.1k
views
voom with combat
limma
voom
combat
batch effect
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
eldronzhou
▴ 10
13
votes
6
replies
6.3k
views
goana limma- extract list of DE genes and genes in the enriched GO terms?
limma
goana
updated 8.9 years ago by
Gordon Smyth
50k • written 8.9 years ago by
carl.mann
▴ 20
13
votes
3
replies
12k
views
Understanding contrasts limma
limma
design and contrast matrix
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
Andy91
▴ 60
13
votes
21
replies
6.1k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma
voom
hurdle
single cell
8.7 years ago
osa.zuta
▴ 40
13
votes
2
replies
6.5k
views
Using limma when continuous and categorical confounders are present at the same time (e.g.age, gender)
limma
covariate
continuous
categorical
adjustment
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
sg45653
• 0
12
votes
6
replies
1.6k
views
Testing for DE genes
affymetrix microarrays
limma
differential gene expression
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
Lennart.Vermander
▴ 10
12
votes
4
replies
4.5k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 5.4 years ago by
Gordon Smyth
50k • written 6.9 years ago by
wd
▴ 30
12
votes
9
replies
8.0k
views
Appropriate use of the function treat of the limma package
limma
treat
microarray
bioconductor
9.2 years ago
svlachavas
▴ 830
12
votes
9
replies
3.3k
views
Limma residuals matrix
limma
updated 4.8 years ago by
Gordon Smyth
50k • written 4.8 years ago by
agustin.gonvi
▴ 20
12
votes
20
replies
2.1k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma
multifactorial design
design and contrast matrix
affymetrix microarrays
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
svlachavas
▴ 830
11
votes
6
replies
3.8k
views
Log fold change on Limma
limma
multiple factor design
updated 8.9 years ago by
Steve Lianoglou
★ 13k • written 8.9 years ago by
ea1402
▴ 20
11
votes
3
replies
9.2k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot
limma
fdr
6.8 years ago • updated 3.5 years ago
tcalvo
▴ 90
11
votes
9
replies
1.6k
views
Correlation of a Linear Variable
limma
limma design matrix
updated 9.1 years ago by
James W. MacDonald
65k • written 9.1 years ago by
andrew.j.skelton73
▴ 370
11
votes
8
replies
10k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
lirongrossmann
▴ 80
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
11
votes
4
replies
1.9k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 7 months ago by
Gordon Smyth
50k • written 5.3 years ago by
tleona3
• 0
11
votes
16
replies
1.8k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma
multifactorial design
diagnostic plots
affymetrix microarrays
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
svlachavas
▴ 830
11
votes
5
replies
13k
views
Limma: how to get same output as topTable but for all the genes ?
limma
toptable
updated 6.8 years ago by
Gordon Smyth
50k • written 15.5 years ago by
Daren Tan
▴ 190
11
votes
3
replies
1.8k
views
Fit a multinomial to RNA-seq count data
voom
limma
glm
multinomial
regression
updated 7.8 years ago by
Robert Castelo
★ 3.3k • written 7.8 years ago by
rubi
▴ 110
11
votes
18
replies
5.0k
views
What is the correct use of removeBatchEffect's design parameter
deseq2
limma
updated 3.2 years ago by
Gordon Smyth
50k • written 3.7 years ago by
Sam
▴ 10
10
votes
4
replies
3.0k
views
Adjust for multiple batches using combat
combat
sva
limma
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
juls
• 0
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
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42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
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42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
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Rsubread counting peaks ATACseq
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