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Showing :
Limma
•
reset
17
votes
14
replies
54k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 3.6 years ago by
OE
• 0 • written 8.5 years ago by
cms72
▴ 20
34
votes
11
replies
45k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 12.1 years ago by
Jon Bråte
▴ 270
33
votes
0
replies
45k
views
limma moderated t-statistics and B-statistics
Microarray
limma
21.3 years ago • updated 5.2 years ago
Gordon Smyth
53k
7
votes
6
replies
31k
views
Conversion of LogFC to FC
limma
logfc
fc
updated 5.9 years ago by
Gordon Smyth
53k • written 5.9 years ago by
nia
▴ 20
8
votes
10
replies
27k
views
Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
10.7 years ago
AurelieMLB
▴ 50
0
votes
7
replies
25k
views
DESeq2 batch correction best practice.
deseq2
limma
RUVSeq
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
94133
• 0
6
votes
3
replies
22k
views
limma p-value and adjusted p-value meaning
limma
10.4 years ago
arfranco
▴ 130
24
votes
11
replies
21k
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 10.0 years ago by
Gordon Smyth
53k • written 10.0 years ago by
lassancejm
▴ 50
10
votes
4
replies
20k
views
Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma
deseq2
updated 6.6 years ago by
Gordon Smyth
53k • written 6.6 years ago by
drowsygoat
▴ 30
21
votes
5
replies
19k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma
voom
updated 10.7 years ago by
Gordon Smyth
53k • written 11.7 years ago by
John Blischak
▴ 190
18
votes
37
replies
19k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
10.6 years ago • updated 10.5 years ago
svlachavas
▴ 840
2
votes
1
reply
18k
views
Installation Problem: installation path not writeable, unable to update packages: MASS, mgcv, rpart
limma
updated 7.9 years ago by
SamGG
▴ 360 • written 7.9 years ago by
ruppmz
• 0
0
votes
2
replies
17k
views
limma, FDR, and p.adjust
limma
limma
updated 3.8 years ago by
Gordon Smyth
53k • written 21.1 years ago by
Kimpel, Mark W
▴ 890
2
votes
5
replies
16k
views
Limma design and contrast matrix question.
Microarray
Regression
limma
Microarray
Regression
limma
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Matthew Thornton
▴ 390
1
vote
5
replies
16k
views
Limma LogFC hand calculation
limma
logfc
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
cookm346
• 0
14
votes
3
replies
15k
views
Understanding contrasts limma
limma
design and contrast matrix
updated 10.3 years ago by
Aaron Lun
★ 29k • written 10.3 years ago by
Andy91
▴ 60
7
votes
1
reply
15k
views
How does limma t-test work?
Bayesian
limma
Bayesian
limma
updated 13.4 years ago by
James W. MacDonald
68k • written 13.4 years ago by
Jorge Miró
▴ 160
9
votes
10
replies
15k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 10.0 years ago by
Bernd Klaus
▴ 610 • written 10.0 years ago by
Ekarl2
▴ 80
12
votes
5
replies
15k
views
Limma: how to get same output as topTable but for all the genes ?
limma
toptable
updated 8.5 years ago by
Gordon Smyth
53k • written 17.1 years ago by
Daren Tan
▴ 190
3
votes
1
reply
14k
views
convert data in to expression set
limma
convert
limma
convert
updated 12.6 years ago by
Jeremy Ng
▴ 180 • written 12.6 years ago by
Nikul Soni
▴ 80
24
votes
12
replies
14k
views
Nanostring analysis with limma
nanostring
limma
updated 10.7 years ago by
ker61
▴ 20 • written 10.7 years ago by
mali salmon
▴ 370
3
votes
5
replies
14k
views
Problem Installing limma package
limma
software error
installation
package installation
updated 8.7 years ago by
Gordon Smyth
53k • written 8.7 years ago by
segador67
• 0
1
vote
12
replies
14k
views
Using limma for quantitative proteomics data
Microarray
Proteomics
limma
Microarray
Proteomics
limma
13.6 years ago
Yong Li
▴ 80
12
votes
3
replies
14k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot
limma
fdr
8.5 years ago • updated 5.2 years ago
tcalvo
▴ 100
28
votes
8
replies
14k
views
Removing continuous covariate effects in limma analysis
limma
microarray
updated 8.3 years ago by
Gordon Smyth
53k • written 10.8 years ago by
Pauly Lin
▴ 160
26
votes
7
replies
13k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma
deseq2
edger
rnaseq
updated 8.3 years ago by
Gordon Smyth
53k • written 8.3 years ago by
Jack
▴ 20
2
votes
6
replies
13k
views
DESeq2 vs limma/voom: PCA completely different. How to proceed?
limma
DESeq2
limma
DESeq2
updated 12.7 years ago by
Simon Anders
★ 3.8k • written 12.7 years ago by
Stephen Turner
▴ 290
6
votes
5
replies
13k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 2.3 years ago by
Gordon Smyth
53k • written 4.2 years ago by
David Lyon
▴ 340
11
votes
8
replies
13k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 8.3 years ago by
Gordon Smyth
53k • written 8.3 years ago by
lirongrossmann
▴ 80
3
votes
6
replies
12k
views
Unable to install "limma" package on RStudio
Bioconductor
limma
limmaGUI
3.9 years ago
jaydengitt
• 0
22
votes
4
replies
12k
views
Correct assumptions of using limma moderated t-test
limma
statistical inference
variance test
bioconductor
updated 10.7 years ago by
Gordon Smyth
53k • written 10.7 years ago by
svlachavas
▴ 840
14
votes
12
replies
12k
views
limma lmFit coefficients and p-values
limma
methylation
ewas
updated 9.5 years ago by
Steve Lianoglou
★ 13k • written 9.5 years ago by
CPR
▴ 30
10
votes
6
replies
12k
views
Estimating and removing batch effects from rna-seq dataset
sva
batch effect
rnaseq
removebatcheffect()
limma
updated 10.2 years ago by
Jeff Leek
▴ 650 • written 10.2 years ago by
AB
▴ 110
9
votes
8
replies
12k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 8.3 years ago by
Gordon Smyth
53k • written 11.5 years ago by
Rao,Xiayu
▴ 550
7
votes
7
replies
11k
views
batch effect : comBat or blocking in limma ?
batch effect
combat
limma
block
updated 10.3 years ago by
Ryan C. Thompson
★ 7.9k • written 10.3 years ago by
eleonoregravier
▴ 70
4
votes
5
replies
11k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 11.2 years ago by
Steve Lianoglou
★ 13k • written 11.2 years ago by
Peter Crisp
▴ 10
1
vote
8
replies
11k
views
"Subscript out of bounds" erorr during microarray analysis with Limma
oligo
limma
bioconductor
affymetrix microarrays
10.5 years ago
Claudia
▴ 10
2
votes
4
replies
11k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma
differential expression
design matrix
error
eset
updated 10.5 years ago by
Aaron Lun
★ 29k • written 10.5 years ago by
Vani
▴ 20
5
votes
8
replies
11k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 21 months ago by
hortense96
• 0 • written 9.4 years ago by
dmcleanuk
▴ 30
8
votes
15
replies
11k
views
Design matrix for continuous independent variable in limma
limma
microarray
10.0 years ago
Linda Chaba
▴ 10
0
votes
3
replies
11k
views
LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
limma
limma
updated 13.3 years ago by
James W. MacDonald
68k • written 13.3 years ago by
Kripa R
▴ 180
5
votes
5
replies
11k
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 10.5 years ago by
Aaron Lun
★ 29k • written 10.5 years ago by
xyliu00
▴ 20
3
votes
2
replies
11k
views
Problem with coefficients that are not estimable (limma)
limma
batch effect
updated 4.7 years ago by
rf
• 0 • written 7.5 years ago by
rrm38
• 0
2
votes
4
replies
11k
views
Limma design and contrast matrix
limma
limma design matrix
limma contrast matrix
9.8 years ago
donny.dw
• 0
3
votes
3
replies
10k
views
TPM data Differential expression analysis
edger
limma
differential gene expression
updated 3.7 years ago by
Gordon Smyth
53k • written 7.7 years ago by
ghmdsr
• 0
3
votes
2
replies
10k
views
Limma paired sample analysis
limma design matrix
limma paired analysis
limma
8.4 years ago
anandprem1792
▴ 20
7
votes
18
replies
10k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
10.3 years ago
Radek
▴ 90
3
votes
3
replies
10k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq
rna-seq
limma
geoquery
edger
updated 8.4 years ago by
Sean Davis
21k • written 8.4 years ago by
hkarakurt
▴ 20
2
votes
2
replies
10k
views
coefficient not estimable (limma warning)
limma
limma
updated 14.7 years ago by
Naomi Altman
★ 6.0k • written 14.7 years ago by
Natasha
▴ 440
9
votes
3
replies
10.0k
views
Limma vs deseq2 results
limma
RNASeq
R
3.6 years ago
k___
▴ 30
4,230 results • Page
1 of 85
Recent ...
Replies
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR
by
Gordon Smyth
53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
JKim
• 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Votes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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