Showing : Limma • reset
17
votes
14
replies
50k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 2.8 years ago by • 0 • written 7.8 years ago by ▴ 20
34
votes
11
replies
43k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 11.4 years ago by ▴ 260
32
votes
0
replies
43k
views
limma moderated t-statistics and B-statistics
Microarray limma
20.6 years ago • updated 4.5 years ago Gordon Smyth 52k
7
votes
6
replies
28k
views
Conversion of LogFC to FC
limma logfc fc
updated 5.1 years ago by 52k • written 5.1 years ago by ▴ 30
8
votes
10
replies
27k
views
Design formula and Design matrix in DESeq
rnaseq deseq2 formula Limma
10.0 years ago • updated 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 43k • written 4.8 years ago by • 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 52k • written 9.2 years ago by ▴ 50
10
votes
4
replies
18k
views
Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma deseq2
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 30
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
9.9 years ago • updated 9.8 years ago svlachavas ▴ 840
21
votes
5
replies
17k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 10.0 years ago by 52k • written 10.9 years ago by ▴ 190
2
votes
1
reply
17k
views
Installation Problem: installation path not writeable, unable to update packages: MASS, mgcv, rpart
limma
updated 7.2 years ago by ▴ 360 • written 7.2 years ago by • 0
0
votes
2
replies
17k
views
limma, FDR, and p.adjust
limma limma
updated 3.1 years ago by 52k • written 20.4 years ago by ▴ 890
2
votes
5
replies
16k
views
Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 11.2 years ago by 68k • written 11.2 years ago by ▴ 380
1
vote
5
replies
15k
views
Limma LogFC hand calculation
limma logfc
updated 9.0 years ago by ★ 28k • written 9.0 years ago by • 0
7
votes
1
reply
15k
views
How does limma t-test work?
Bayesian limma Bayesian limma
updated 12.6 years ago by 68k • written 12.7 years ago by ▴ 160
12
votes
5
replies
14k
views
Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 7.8 years ago by 52k • written 16.4 years ago by ▴ 190
13
votes
3
replies
14k
views
Understanding contrasts limma
limma design and contrast matrix
updated 9.5 years ago by ★ 28k • written 9.5 years ago by ▴ 60
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 9.3 years ago by ▴ 610 • written 9.3 years ago by ▴ 80
3
votes
1
reply
14k
views
convert data in to expression set
limma convert limma convert
updated 11.8 years ago by ▴ 180 • written 11.8 years ago by ▴ 80
3
votes
5
replies
13k
views
Problem Installing limma package
limma software error installation package installation
updated 8.0 years ago by 52k • written 8.0 years ago by • 0
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
24
votes
12
replies
13k
views
Nanostring analysis with limma
nanostring limma
updated 10.0 years ago by ▴ 20 • written 10.0 years ago by ▴ 370
28
votes
8
replies
13k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 7.6 years ago by 52k • written 10.1 years ago by ▴ 160
2
votes
6
replies
13k
views
DESeq2 vs limma/voom: PCA completely different. How to proceed?
limma DESeq2 limma DESeq2
updated 12.0 years ago by ★ 3.8k • written 12.0 years ago by ▴ 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 4.4 years ago tcalvo ▴ 100
11
votes
8
replies
12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.6 years ago by 52k • written 7.6 years ago by ▴ 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 7.6 years ago by 52k • written 7.6 years ago by ▴ 20
22
votes
4
replies
11k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 9.9 years ago by 52k • written 9.9 years ago by ▴ 840
10
votes
6
replies
11k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 9.5 years ago by ▴ 650 • written 9.5 years ago by ▴ 110
3
votes
6
replies
11k
views
Unable to install "limma" package on RStudio
Bioconductor limma limmaGUI
3.2 years ago jaydengitt • 0
14
votes
12
replies
11k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 8.7 years ago by ★ 13k • written 8.7 years ago by ▴ 30
6
votes
5
replies
11k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 19 months ago by 52k • written 3.5 years ago by ▴ 340
9
votes
8
replies
11k
views
removeBatchEffect options: design and covariates
limma removebatcheffect
updated 7.6 years ago by 52k • written 10.7 years ago by ▴ 550
0
votes
3
replies
10k
views
LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
limma limma
updated 12.6 years ago by 68k • written 12.6 years ago by ▴ 180
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 9.8 years ago by ★ 28k • written 9.8 years ago by ▴ 20
5
votes
8
replies
10k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 12 months ago by • 0 • written 8.7 years ago by ▴ 30
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 9.8 years ago by ★ 28k • written 9.8 years ago by ▴ 20
4
votes
5
replies
10k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 10.5 years ago by ★ 13k • written 10.5 years ago by ▴ 10
8
votes
15
replies
10k
views
Design matrix for continuous independent variable in limma
limma microarray
9.3 years ago Linda Chaba ▴ 10
1
vote
8
replies
10k
views
"Subscript out of bounds" erorr during microarray analysis with Limma
oligo limma bioconductor affymetrix microarrays
9.8 years ago Claudia ▴ 10
3
votes
2
replies
10k
views
Limma paired sample analysis
limma design matrix limma paired analysis limma
7.6 years ago anandprem1792 ▴ 20
3
votes
2
replies
10.0k
views
Problem with coefficients that are not estimable (limma)
limma batch effect
updated 3.9 years ago by • 0 • written 6.8 years ago by • 0
2
votes
2
replies
10.0k
views
coefficient not estimable (limma warning)
limma limma
updated 14.0 years ago by ★ 6.0k • written 14.0 years ago by ▴ 440
7
votes
7
replies
9.9k
views
batch effect : comBat or blocking in limma ?
batch effect combat limma block
updated 9.6 years ago by ★ 7.9k • written 9.6 years ago by ▴ 70
2
votes
4
replies
9.8k
views
Limma design and contrast matrix
limma limma design matrix limma contrast matrix
9.1 years ago donny.dw • 0
3
votes
3
replies
9.7k
views
TPM data Differential expression analysis
edger limma differential gene expression
updated 2.9 years ago by 52k • written 7.0 years ago by • 0
7
votes
18
replies
9.6k
views
Differential expression analysis: Continuous variables
DESeq EdgeR limma
9.6 years ago Radek ▴ 90
10
votes
11
replies
9.1k
views
Standard error and effect size from Limma
effect size Limma toptable Standard Error
updated 9.8 years ago by 52k • written 9.8 years ago by ▴ 20
13
votes
9
replies
9.1k
views
Appropriate use of the function treat of the limma package
limma treat microarray bioconductor
10.1 years ago svlachavas ▴ 840
50 results • Page 1 of 1
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Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - I appreciate the mathematical explanation and link to Dr. Phipson's thesis!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - this is very clear!
Answer: How do I set up my DESeq analysis when I know a few vehicle control samples prov by Michael Love 43k
I think it will capture it automatically. E.g. if you use the method that focuses on genes lowly or not affected by the treatment, then the…
Votes
Comment: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
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