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Showing :
Limma
•
reset
17
votes
14
replies
49k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 2.7 years ago by
OE
• 0 • written 7.7 years ago by
cms72
▴ 20
34
votes
11
replies
42k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 11.3 years ago by
Jon Bråte
▴ 260
32
votes
0
replies
42k
views
limma moderated t-statistics and B-statistics
Microarray
limma
20.5 years ago • updated 4.4 years ago
Gordon Smyth
52k
7
votes
6
replies
27k
views
Conversion of LogFC to FC
limma
logfc
fc
updated 5.0 years ago by
Gordon Smyth
52k • written 5.0 years ago by
nia
▴ 30
8
votes
10
replies
26k
views
Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
9.9 years ago
AurelieMLB
▴ 50
0
votes
7
replies
24k
views
DESeq2 batch correction best practice.
deseq2
limma
RUVSeq
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
94133
• 0
6
votes
3
replies
20k
views
limma p-value and adjusted p-value meaning
limma
9.6 years ago
arfranco
▴ 130
24
votes
11
replies
20k
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 9.2 years ago by
Gordon Smyth
52k • written 9.2 years ago by
lassancejm
▴ 50
18
votes
37
replies
18k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
9.8 years ago • updated 9.7 years ago
svlachavas
▴ 840
10
votes
4
replies
17k
views
Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma
deseq2
updated 5.8 years ago by
Gordon Smyth
52k • written 5.8 years ago by
drowsygoat
▴ 30
2
votes
1
reply
17k
views
Installation Problem: installation path not writeable, unable to update packages: MASS, mgcv, rpart
limma
updated 7.1 years ago by
SamGG
▴ 360 • written 7.1 years ago by
ruppmz
• 0
21
votes
5
replies
17k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma
voom
updated 9.9 years ago by
Gordon Smyth
52k • written 10.8 years ago by
John Blischak
▴ 190
0
votes
2
replies
17k
views
limma, FDR, and p.adjust
limma
limma
updated 3.0 years ago by
Gordon Smyth
52k • written 20.3 years ago by
Kimpel, Mark W
▴ 890
2
votes
5
replies
15k
views
Limma design and contrast matrix question.
Microarray
Regression
limma
Microarray
Regression
limma
updated 11.2 years ago by
James W. MacDonald
68k • written 11.2 years ago by
Matthew Thornton
▴ 380
1
vote
5
replies
15k
views
Limma LogFC hand calculation
limma
logfc
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
cookm346
• 0
7
votes
1
reply
14k
views
How does limma t-test work?
Bayesian
limma
Bayesian
limma
updated 12.6 years ago by
James W. MacDonald
68k • written 12.6 years ago by
Jorge Miró
▴ 160
12
votes
5
replies
14k
views
Limma: how to get same output as topTable but for all the genes ?
limma
toptable
updated 7.7 years ago by
Gordon Smyth
52k • written 16.3 years ago by
Daren Tan
▴ 190
13
votes
3
replies
14k
views
Understanding contrasts limma
limma
design and contrast matrix
updated 9.5 years ago by
Aaron Lun
★ 28k • written 9.5 years ago by
Andy91
▴ 60
3
votes
1
reply
14k
views
convert data in to expression set
limma
convert
limma
convert
updated 11.8 years ago by
Jeremy Ng
▴ 180 • written 11.8 years ago by
Nikul Soni
▴ 80
9
votes
10
replies
14k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 9.2 years ago by
Bernd Klaus
▴ 610 • written 9.2 years ago by
Ekarl2
▴ 80
1
vote
12
replies
13k
views
Using limma for quantitative proteomics data
Microarray
Proteomics
limma
Microarray
Proteomics
limma
12.8 years ago
Yong Li
▴ 80
3
votes
5
replies
13k
views
Problem Installing limma package
limma
software error
installation
package installation
updated 7.9 years ago by
Gordon Smyth
52k • written 7.9 years ago by
segador67
• 0
24
votes
12
replies
13k
views
Nanostring analysis with limma
nanostring
limma
updated 9.9 years ago by
ker61
▴ 20 • written 9.9 years ago by
mali salmon
▴ 370
28
votes
8
replies
13k
views
Removing continuous covariate effects in limma analysis
limma
microarray
updated 7.5 years ago by
Gordon Smyth
52k • written 10.0 years ago by
Pauly Lin
▴ 160
2
votes
6
replies
13k
views
DESeq2 vs limma/voom: PCA completely different. How to proceed?
limma
DESeq2
limma
DESeq2
updated 11.9 years ago by
Simon Anders
★ 3.8k • written 11.9 years ago by
Stephen Turner
▴ 290
12
votes
3
replies
12k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot
limma
fdr
7.7 years ago • updated 4.3 years ago
tcalvo
▴ 100
11
votes
8
replies
12k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 7.5 years ago by
Gordon Smyth
52k • written 7.5 years ago by
lirongrossmann
▴ 80
25
votes
7
replies
12k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 7.5 years ago by
Gordon Smyth
52k • written 7.5 years ago by
Jack
▴ 20
22
votes
4
replies
11k
views
Correct assumptions of using limma moderated t-test
limma
statistical inference
variance test
bioconductor
updated 9.8 years ago by
Gordon Smyth
52k • written 9.8 years ago by
svlachavas
▴ 840
10
votes
6
replies
11k
views
Estimating and removing batch effects from rna-seq dataset
sva
batch effect
rnaseq
removebatcheffect()
limma
updated 9.4 years ago by
Jeff Leek
▴ 650 • written 9.4 years ago by
AB
▴ 110
14
votes
12
replies
11k
views
limma lmFit coefficients and p-values
limma
methylation
ewas
updated 8.6 years ago by
Steve Lianoglou
★ 13k • written 8.6 years ago by
CPR
▴ 30
3
votes
6
replies
11k
views
Unable to install "limma" package on RStudio
Bioconductor
limma
limmaGUI
3.1 years ago
jaydengitt
• 0
6
votes
5
replies
11k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 18 months ago by
Gordon Smyth
52k • written 3.4 years ago by
David Lyon
▴ 340
0
votes
3
replies
10k
views
LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
limma
limma
updated 12.5 years ago by
James W. MacDonald
68k • written 12.5 years ago by
Kripa R
▴ 180
9
votes
8
replies
10k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 7.5 years ago by
Gordon Smyth
52k • written 10.6 years ago by
Rao,Xiayu
▴ 550
2
votes
4
replies
10k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma
differential expression
design matrix
error
eset
updated 9.7 years ago by
Aaron Lun
★ 28k • written 9.7 years ago by
Vani
▴ 20
5
votes
5
replies
10k
views
How to make contrast table to combine two conditions/treatments against another one (in a multi groups experiments
limma
design and contrast matrix
updated 9.7 years ago by
Aaron Lun
★ 28k • written 9.7 years ago by
xyliu00
▴ 20
5
votes
8
replies
10k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 11 months ago by
hortense96
• 0 • written 8.6 years ago by
dmcleanuk
▴ 30
8
votes
15
replies
10.0k
views
Design matrix for continuous independent variable in limma
limma
microarray
9.2 years ago
Linda Chaba
▴ 10
4
votes
5
replies
10.0k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 10.4 years ago by
Steve Lianoglou
★ 13k • written 10.4 years ago by
Peter Crisp
▴ 10
2
votes
2
replies
9.9k
views
coefficient not estimable (limma warning)
limma
limma
updated 13.9 years ago by
Naomi Altman
★ 6.0k • written 13.9 years ago by
Natasha
▴ 440
1
vote
8
replies
9.9k
views
"Subscript out of bounds" erorr during microarray analysis with Limma
oligo
limma
bioconductor
affymetrix microarrays
9.7 years ago
Claudia
▴ 10
3
votes
2
replies
9.9k
views
Limma paired sample analysis
limma design matrix
limma paired analysis
limma
7.5 years ago
anandprem1792
▴ 20
3
votes
2
replies
9.8k
views
Problem with coefficients that are not estimable (limma)
limma
batch effect
updated 3.9 years ago by
rf
• 0 • written 6.7 years ago by
rrm38
• 0
2
votes
4
replies
9.7k
views
Limma design and contrast matrix
limma
limma design matrix
limma contrast matrix
9.0 years ago
donny.dw
• 0
7
votes
7
replies
9.7k
views
batch effect : comBat or blocking in limma ?
batch effect
combat
limma
block
updated 9.5 years ago by
Ryan C. Thompson
★ 7.9k • written 9.5 years ago by
eleonoregravier
▴ 70
3
votes
3
replies
9.6k
views
TPM data Differential expression analysis
edger
limma
differential gene expression
updated 2.9 years ago by
Gordon Smyth
52k • written 6.9 years ago by
ghmdsr
• 0
7
votes
18
replies
9.5k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
9.5 years ago
Radek
▴ 90
10
votes
11
replies
9.0k
views
Standard error and effect size from Limma
effect size
Limma
toptable
Standard Error
updated 9.7 years ago by
Gordon Smyth
52k • written 9.7 years ago by
Vani
▴ 20
13
votes
9
replies
9.0k
views
Appropriate use of the function treat of the limma package
limma
treat
microarray
bioconductor
10.0 years ago
svlachavas
▴ 840
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Comment: Bioconductor unable to update 'curl'
by
kagodwi2
• 0
UPDATE: I was able to get curl to work! It seems that because the new version was literally JUST released, there is something "funky" goin…
Comment: Bioconductor unable to update 'curl'
by
kagodwi2
• 0
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Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
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