Showing : limma • reset
17
votes
14
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57k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 3.7 years ago by • 0 • written 8.6 years ago by ▴ 20
34
votes
11
replies
46k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 12.3 years ago by ▴ 270
33
votes
0
replies
46k
views
limma moderated t-statistics and B-statistics
Microarray limma
21.5 years ago • updated 5.4 years ago Gordon Smyth 53k
7
votes
6
replies
31k
views
Conversion of LogFC to FC
limma logfc fc
updated 6.0 years ago by 53k • written 6.0 years ago by ▴ 20
8
votes
10
replies
28k
views
Design formula and Design matrix in DESeq
rnaseq deseq2 formula Limma
10.8 years ago AurelieMLB ▴ 50
0
votes
7
replies
25k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
6
votes
3
replies
23k
views
limma p-value and adjusted p-value meaning
limma
10.5 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 10.1 years ago by 53k • written 10.1 years ago by ▴ 50
10
votes
4
replies
21k
views
Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma deseq2
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 30
21
votes
5
replies
20k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 10.8 years ago by 53k • written 11.8 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
10.8 years ago • updated 10.6 years ago svlachavas ▴ 840
0
votes
2
replies
18k
views
limma, FDR, and p.adjust
limma limma
updated 3.9 years ago by 53k • written 21.2 years ago by ▴ 890
2
votes
1
reply
18k
views
Installation Problem: installation path not writeable, unable to update packages: MASS, mgcv, rpart
limma
updated 8.1 years ago by ▴ 360 • written 8.1 years ago by • 0
2
votes
5
replies
16k
views
Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 12.1 years ago by 68k • written 12.1 years ago by ▴ 390
1
vote
5
replies
16k
views
Limma LogFC hand calculation
limma logfc
updated 9.8 years ago by ★ 29k • written 9.8 years ago by • 0
14
votes
3
replies
16k
views
Understanding contrasts limma
limma design and contrast matrix
updated 10.4 years ago by ★ 29k • written 10.4 years ago by ▴ 60
7
votes
1
reply
15k
views
How does limma t-test work?
Bayesian limma Bayesian limma
updated 13.5 years ago by 68k • written 13.5 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 10.2 years ago by ▴ 610 • written 10.2 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 8.6 years ago by 53k • written 17.3 years ago by ▴ 190
12
votes
3
replies
15k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot limma fdr
8.6 years ago • updated 5.3 years ago tcalvo ▴ 100
3
votes
1
reply
14k
views
convert data in to expression set
limma convert limma convert
updated 12.7 years ago by ▴ 180 • written 12.7 years ago by ▴ 80
24
votes
12
replies
14k
views
Nanostring analysis with limma
nanostring limma
updated 10.9 years ago by ▴ 20 • written 10.9 years ago by ▴ 370
6
votes
5
replies
14k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 2.5 years ago by 53k • written 4.4 years ago by ▴ 340
3
votes
5
replies
14k
views
Problem Installing limma package
limma software error installation package installation
updated 8.9 years ago by 53k • written 8.9 years ago by • 0
28
votes
8
replies
14k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 8.5 years ago by 53k • written 11.0 years ago by ▴ 160
1
vote
12
replies
14k
views
Using limma for quantitative proteomics data
Microarray Proteomics limma Microarray Proteomics limma
13.7 years ago Yong Li ▴ 80
26
votes
7
replies
14k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 20
11
votes
8
replies
14k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 80
2
votes
6
replies
14k
views
DESeq2 vs limma/voom: PCA completely different. How to proceed?
limma DESeq2 limma DESeq2
updated 12.9 years ago by ★ 3.8k • written 12.9 years ago by ▴ 290
3
votes
6
replies
13k
views
Unable to install "limma" package on RStudio
Bioconductor limma limmaGUI
4.1 years ago jaydengitt • 0
14
votes
12
replies
13k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 30
22
votes
4
replies
13k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 10.8 years ago by 53k • written 10.8 years ago by ▴ 840
9
votes
8
replies
12k
views
removeBatchEffect options: design and covariates
limma removebatcheffect
updated 8.5 years ago by 53k • written 11.6 years ago by ▴ 550
3
votes
3
replies
12k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 8.6 years ago by 21k • written 8.6 years ago by ▴ 20
10
votes
6
replies
12k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 10.4 years ago by ▴ 650 • written 10.4 years ago by ▴ 110
7
votes
7
replies
12k
views
batch effect : comBat or blocking in limma ?
batch effect combat limma block
updated 10.5 years ago by ★ 7.9k • written 10.5 years ago by ▴ 70
1
vote
8
replies
12k
views
"Subscript out of bounds" erorr during microarray analysis with Limma
oligo limma bioconductor affymetrix microarrays
10.7 years ago Claudia ▴ 10
4
votes
5
replies
11k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 11.4 years ago by ★ 13k • written 11.4 years ago by ▴ 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 10.7 years ago by ★ 29k • written 10.7 years ago by ▴ 20
5
votes
8
replies
11k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 23 months ago by • 0 • written 9.6 years ago by ▴ 30
8
votes
15
replies
11k
views
Design matrix for continuous independent variable in limma
limma microarray
10.2 years ago Linda Chaba ▴ 10
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 10.7 years ago by ★ 29k • written 10.7 years ago by ▴ 20
0
votes
3
replies
11k
views
LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
limma limma
updated 13.4 years ago by 68k • written 13.4 years ago by ▴ 180
3
votes
2
replies
11k
views
Problem with coefficients that are not estimable (limma)
limma batch effect
updated 4.8 years ago by • 0 • written 7.7 years ago by • 0
9
votes
3
replies
11k
views
Limma vs deseq2 results
limma RNASeq R
3.8 years ago k___ ▴ 30
3
votes
3
replies
11k
views
TPM data Differential expression analysis
edger limma differential gene expression
updated 3.8 years ago by 53k • written 7.9 years ago by • 0
2
votes
4
replies
11k
views
Limma design and contrast matrix
limma limma design matrix limma contrast matrix
10.0 years ago donny.dw • 0
3
votes
2
replies
11k
views
Limma paired sample analysis
limma design matrix limma paired analysis limma
8.5 years ago anandprem1792 ▴ 20
7
votes
18
replies
10k
views
Differential expression analysis: Continuous variables
DESeq EdgeR limma
10.5 years ago Radek ▴ 90
2
votes
2
replies
10k
views
coefficient not estimable (limma warning)
limma limma
updated 14.8 years ago by ★ 6.0k • written 14.8 years ago by ▴ 440
4,233 results • Page 1 of 85
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Answer: Is it still possible to do batch correction for my data? by Gordon Smyth 53k
I agree with the comments from James MacDonald, but I will add that if you use the standard linear model correction for batch ``` design <-…
Answer: specifying refColumn in calcNormFactors() by Gordon Smyth 53k
Your question is about cross-validation rather than specifically about edgeR. A general principle of cross-validation is that you must norm…
Answer: Sex prediction in sesame for EPICV2 by Tim Peters ▴ 230
Hi Pooja, There is a tutorial for preprocessing EPICv2 via sesame here: https://clark-lab.github.io/EPICv2_tutorial/. There is no call t…
Comment: Convergence Issues and Model Selection DESeq2 by dani.guan.3 • 0
Thank you, I appreciate your time and help.
Comment: Convergence Issues and Model Selection DESeq2 by Michael Love 43k
> out of my 30,229 genes, 795 (2.6%) are better explained ... Not exactly. Frequentist statistics is not symmetric in this way. If it were…
Votes
DiffBind dropping peaks in ATAC-seq data
A: decideTests() options in LIMMA
A: Removing cell cycle genes in large data set integration
A: Removing cell cycle genes in large data set integration
Answer: Quick two questions on limpa
Awards • All
Teacher to Gordon Smyth 53k
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Popular Question to James W. MacDonald 68k
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