Showing : Limma • reset
17
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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 • 0 • written 8.5 years ago by ▴ 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 ▴ 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 53k • written 5.9 years ago by ▴ 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 43k • written 5.6 years ago by • 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 53k • written 10.0 years ago by ▴ 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 53k • written 6.6 years ago by ▴ 30
21
votes
5
replies
19k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 10.7 years ago by 53k • written 11.7 years ago by ▴ 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 ▴ 360 • written 7.9 years ago by • 0
0
votes
2
replies
17k
views
limma, FDR, and p.adjust
limma limma
updated 3.8 years ago by 53k • written 21.1 years ago by ▴ 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 68k • written 12.0 years ago by ▴ 390
1
vote
5
replies
16k
views
Limma LogFC hand calculation
limma logfc
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
14
votes
3
replies
15k
views
Understanding contrasts limma
limma design and contrast matrix
updated 10.3 years ago by ★ 29k • written 10.3 years ago by ▴ 60
7
votes
1
reply
15k
views
How does limma t-test work?
Bayesian limma Bayesian limma
updated 13.4 years ago by 68k • written 13.4 years ago by ▴ 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 ▴ 610 • written 10.0 years ago by ▴ 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 53k • written 17.1 years ago by ▴ 190
3
votes
1
reply
14k
views
convert data in to expression set
limma convert limma convert
updated 12.6 years ago by ▴ 180 • written 12.6 years ago by ▴ 80
24
votes
12
replies
14k
views
Nanostring analysis with limma
nanostring limma
updated 10.7 years ago by ▴ 20 • written 10.7 years ago by ▴ 370
3
votes
5
replies
14k
views
Problem Installing limma package
limma software error installation package installation
updated 8.7 years ago by 53k • written 8.7 years ago by • 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 53k • written 10.8 years ago by ▴ 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 53k • written 8.3 years ago by ▴ 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 ★ 3.8k • written 12.7 years ago by ▴ 290
6
votes
5
replies
13k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 2.3 years ago by 53k • written 4.2 years ago by ▴ 340
11
votes
8
replies
13k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 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 53k • written 10.7 years ago by ▴ 840
14
votes
12
replies
12k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 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 ▴ 650 • written 10.2 years ago by ▴ 110
9
votes
8
replies
12k
views
removeBatchEffect options: design and covariates
limma removebatcheffect
updated 8.3 years ago by 53k • written 11.5 years ago by ▴ 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 ★ 7.9k • written 10.3 years ago by ▴ 70
4
votes
5
replies
11k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 11.2 years ago by ★ 13k • written 11.2 years ago by ▴ 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 ★ 29k • written 10.5 years ago by ▴ 20
5
votes
8
replies
11k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 21 months ago by • 0 • written 9.4 years ago by ▴ 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 68k • written 13.3 years ago by ▴ 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 ★ 29k • written 10.5 years ago by ▴ 20
3
votes
2
replies
11k
views
Problem with coefficients that are not estimable (limma)
limma batch effect
updated 4.7 years ago by • 0 • written 7.5 years ago by • 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 53k • written 7.7 years ago by • 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 21k • written 8.4 years ago by ▴ 20
2
votes
2
replies
10k
views
coefficient not estimable (limma warning)
limma limma
updated 14.7 years ago by ★ 6.0k • written 14.7 years ago by ▴ 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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