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limma
•
reset
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 22 months ago by
OE
• 0 • written 6.8 years ago by
cms72
▴ 20
32
votes
0
replies
38k
views
limma moderated t-statistics and B-statistics
Microarray
limma
19.6 years ago • updated 3.5 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 12 months ago by
manuelsokolov
• 0 • written 10.5 years ago by
Jon Bråte
▴ 250
8
votes
10
replies
25k
views
Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
9.0 years ago
AurelieMLB
▴ 50
0
votes
7
replies
21k
views
DESeq2 batch correction best practice.
deseq2
limma
RUVSeq
updated 3.9 years ago by
Michael Love
42k • written 3.9 years ago by
94133
• 0
7
votes
6
replies
20k
views
Conversion of LogFC to FC
limma
logfc
fc
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
nia
▴ 30
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
6
votes
3
replies
18k
views
limma p-value and adjusted p-value meaning
limma
8.7 years ago
arfranco
▴ 130
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
8.9 years ago • updated 8.8 years ago
svlachavas
▴ 830
2
votes
1
reply
16k
views
Installation Problem: installation path not writeable, unable to update packages: MASS, mgcv, rpart
limma
updated 6.2 years ago by
SamGG
▴ 350 • written 6.2 years ago by
ruppmz
• 0
0
votes
2
replies
15k
views
limma, FDR, and p.adjust
limma
limma
updated 2.1 years ago by
Gordon Smyth
50k • written 19.4 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 10.3 years ago by
James W. MacDonald
65k • written 10.3 years ago by
Matthew Thornton
▴ 350
21
votes
5
replies
14k
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
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
3
votes
1
reply
13k
views
convert data in to expression set
limma
convert
limma
convert
updated 10.9 years ago by
Jeremy Ng
▴ 180 • written 10.9 years ago by
Nikul Soni
▴ 80
10
votes
4
replies
13k
views
Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma
deseq2
updated 4.9 years ago by
Gordon Smyth
50k • written 4.9 years ago by
drowsygoat
▴ 30
9
votes
10
replies
13k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 8.3 years ago by
Bernd Klaus
▴ 610 • written 8.3 years ago by
Ekarl2
▴ 80
1
vote
5
replies
13k
views
Limma LogFC hand calculation
limma
logfc
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
cookm346
• 0
1
vote
12
replies
12k
views
Using limma for quantitative proteomics data
Microarray
Proteomics
limma
Microarray
Proteomics
limma
11.9 years ago
Yong Li
▴ 80
7
votes
1
reply
12k
views
How does limma t-test work?
Bayesian
limma
Bayesian
limma
updated 11.7 years ago by
James W. MacDonald
65k • written 11.7 years ago by
Jorge Miró
▴ 160
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
24
votes
12
replies
12k
views
Nanostring analysis with limma
nanostring
limma
updated 9.0 years ago by
ker61
▴ 20 • written 9.0 years ago by
mali salmon
▴ 370
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
2
votes
6
replies
12k
views
DESeq2 vs limma/voom: PCA completely different. How to proceed?
limma
DESeq2
limma
DESeq2
updated 11.1 years ago by
Simon Anders
★ 3.7k • written 11.1 years ago by
Stephen Turner
▴ 290
3
votes
5
replies
10k
views
Problem Installing limma package
limma
software error
installation
package installation
updated 7.0 years ago by
Gordon Smyth
50k • written 7.0 years ago by
segador67
• 0
10
votes
6
replies
10k
views
Estimating and removing batch effects from rna-seq dataset
sva
batch effect
rnaseq
removebatcheffect()
limma
updated 8.6 years ago by
Jeff Leek
▴ 650 • written 8.6 years ago by
AB
▴ 110
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
22
votes
4
replies
9.9k
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
0
votes
3
replies
9.8k
views
LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
limma
limma
updated 11.6 years ago by
James W. MacDonald
65k • written 11.6 years ago by
Kripa R
▴ 180
21
votes
7
replies
9.6k
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
14
votes
12
replies
9.3k
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
2
votes
2
replies
9.3k
views
coefficient not estimable (limma warning)
limma
limma
updated 13.0 years ago by
Naomi Altman
★ 6.0k • written 13.0 years ago by
Natasha
▴ 440
5
votes
5
replies
9.2k
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 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
xyliu00
▴ 20
11
votes
3
replies
9.1k
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
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 16 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
1
vote
8
replies
8.8k
views
"Subscript out of bounds" erorr during microarray analysis with Limma
oligo
limma
bioconductor
affymetrix microarrays
8.8 years ago
Claudia
▴ 10
8
votes
15
replies
8.7k
views
Design matrix for continuous independent variable in limma
limma
microarray
8.3 years ago
Linda Chaba
▴ 10
9
votes
8
replies
8.6k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 6.7 years ago by
Gordon Smyth
50k • written 9.8 years ago by
Rao,Xiayu
▴ 550
3
votes
5
replies
8.6k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 9.5 years ago by
Steve Lianoglou
★ 13k • written 9.5 years ago by
Peter Crisp
▴ 10
3
votes
2
replies
8.5k
views
Limma paired sample analysis
limma design matrix
limma paired analysis
limma
6.7 years ago
anandprem1792
▴ 20
2
votes
4
replies
8.5k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma
differential expression
design matrix
error
eset
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
Vani
▴ 20
1
vote
3
replies
8.4k
views
Annotating limma Results with Gene Names for Affy Microarrays
limma
annotation
pd.mogene.2.0.st
mogene20sttranscriptcluster.db
affy
updated 9.4 years ago by
Gordon Smyth
50k • written 9.4 years ago by
alakatos
▴ 130
0
votes
5
replies
8.4k
views
Limma topTable; fold changes look completely different to the normalized data and Limma fold change
limma
limma
11.8 years ago
john herbert
▴ 560
7
votes
7
replies
8.4k
views
batch effect : comBat or blocking in limma ?
batch effect
combat
limma
block
updated 8.6 years ago by
Ryan C. Thompson
★ 7.9k • written 8.6 years ago by
eleonoregravier
▴ 70
2
votes
4
replies
8.3k
views
Limma design and contrast matrix
limma
limma design matrix
limma contrast matrix
8.1 years ago
donny.dw
• 0
7
votes
18
replies
8.3k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
8.6 years ago
Radek
▴ 90
3
votes
3
replies
8.1k
views
TPM data Differential expression analysis
edger
limma
differential gene expression
updated 24 months ago by
Gordon Smyth
50k • written 6.0 years ago by
ghmdsr
• 0
4
votes
4
replies
8.1k
views
edgeR design matrix and contrasts: how to make contrast between groups that aren't shown in the design matrix columns?
edger
design and contrast matrix
contrast
limma contrast matrix
limma
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
cafelumiere12
▴ 20
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
3
votes
2
replies
7.8k
views
Problem with coefficients that are not estimable (limma)
limma
batch effect
updated 3.0 years ago by
rf
• 0 • written 5.8 years ago by
rrm38
• 0
50 results • Page
1 of 1
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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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