Showing : Limma • reset
26
votes
8
replies
9.3k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 4.7 years ago by 45k • written 7.2 years ago by ▴ 120
25
votes
9
replies
5.0k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 7.3 years ago by 45k • written 7.3 years ago by ▴ 40
25
votes
0
replies
29k
views
limma moderated t-statistics and B-statistics
Microarray limma
17.7 years ago • updated 19 months ago Gordon Smyth 45k
22
votes
4
replies
7.8k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 7.0 years ago by 45k • written 7.0 years ago by ▴ 780
21
votes
12
replies
9.9k
views
Nanostring analysis with limma
nanostring limma
updated 7.1 years ago by ▴ 20 • written 7.1 years ago by ▴ 350
20
votes
7
replies
5.0k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 4.7 years ago by 45k • written 4.7 years ago by • 0
20
votes
5
replies
9.8k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 7.0 years ago by 45k • written 8.0 years ago by ▴ 180
19
votes
9
replies
26k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
updated 3 months ago by • 0 • written 8.5 years ago by ▴ 190
19
votes
10
replies
3.1k
views
Do the outputs of Limma's competitive gene set methods (camera, romer) require a mutliple testing correction?
limma romer
updated 6.8 years ago by 45k • written 6.8 years ago by ▴ 40
18
votes
37
replies
15k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
7.0 years ago • updated 6.9 years ago svlachavas ▴ 780
18
votes
3
replies
1.8k
views
cameraPR vs geneSetTest and ROAST/CAMERA in general
limma voomwithqualityweights gene set analysis
updated 4.2 years ago by ★ 27k • written 4.2 years ago by ▴ 70
17
votes
8
replies
2.8k
views
Limma camera function never gives any differentially expressed gene sets
limma
updated 4.8 years ago by • 0 • written 6.9 years ago by ▴ 400
17
votes
18
replies
3.5k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 6.6 years ago by ▴ 840 • written 6.7 years ago by ▴ 780
17
votes
11
replies
14k
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 6.3 years ago by 45k • written 6.3 years ago by ▴ 40
16
votes
5
replies
2.3k
views
limma voom Mean-variance trend plot: x-axis?
limma
3.1 years ago AS ▴ 70
16
votes
13
replies
2.2k
views
Camera and ROAST
limma
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 30
15
votes
14
replies
2.5k
views
extract similar expressed genes (SEGs) rather than DEGs
limma microarray
updated 7.3 years ago by 21k • written 7.4 years ago by ▴ 340
15
votes
6
replies
2.2k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 5.8 years ago by ▴ 90 • written 5.8 years ago by ▴ 140
15
votes
7
replies
3.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 6.0 years ago by 7.8k • written 6.0 years ago by • 0
15
votes
4
replies
1.8k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 5.9 years ago by 7.8k • written 5.9 years ago by ▴ 130
15
votes
5
replies
5.8k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 6.5 years ago by 45k • written 6.5 years ago by ▴ 100
14
votes
13
replies
22k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 4.9 years ago by ★ 27k • written 4.9 years ago by ▴ 20
14
votes
12
replies
6.2k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 5.8 years ago by 13k • written 5.8 years ago by ▴ 30
14
votes
16
replies
1.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
6.0 years ago giroudpaul ▴ 40
14
votes
16
replies
1.8k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 6.9 years ago by 60k • written 6.9 years ago by ▴ 10
14
votes
9
replies
2.6k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 4.3 years ago by ▴ 120 • written 6.1 years ago by ▴ 80
13
votes
0
replies
2.5k
views
simultaneous use of robust and weighting methods in limma
limma robust arrayWeights
8.5 years ago • updated 6.0 years ago Gordon Smyth 45k
13
votes
21
replies
4.6k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma voom hurdle single cell
6.7 years ago osa.zuta ▴ 40
13
votes
3
replies
8.8k
views
Understanding contrasts limma
limma design and contrast matrix
updated 6.6 years ago by ★ 27k • written 6.6 years ago by ▴ 60
13
votes
2
replies
2.3k
views
voom with combat
limma voom combat batch effect
updated 5.8 years ago by 45k • written 5.8 years ago by ▴ 10
13
votes
2
replies
5.1k
views
Using limma when continuous and categorical confounders are present at the same time (e.g.age, gender)
limma covariate continuous categorical adjustment
updated 6.9 years ago by 45k • written 6.9 years ago by • 0
13
votes
6
replies
5.1k
views
goana limma- extract list of DE genes and genes in the enriched GO terms?
limma goana
updated 6.9 years ago by 45k • written 6.9 years ago by ▴ 20
12
votes
9
replies
5.9k
views
Appropriate use of the function treat of the limma package
limma treat microarray bioconductor
7.2 years ago svlachavas ▴ 780
12
votes
4
replies
3.3k
views
differential expression analysis of htseq data with edgeR/voom
voom htseq edgeR limma RNASeq123
updated 3.4 years ago by 45k • written 5.0 years ago by ▴ 30
12
votes
9
replies
1.3k
views
Limma residuals matrix
limma
updated 2.8 years ago by 45k • written 2.8 years ago by ▴ 10
12
votes
20
replies
1.5k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 6.7 years ago by ★ 27k • written 6.7 years ago by ▴ 780
12
votes
6
replies
957
views
Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 5.0 years ago by ★ 27k • written 5.0 years ago by ▴ 10
11
votes
16
replies
1.4k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma multifactorial design diagnostic plots affymetrix microarrays
updated 6.7 years ago by 60k • written 6.7 years ago by ▴ 780
11
votes
6
replies
2.6k
views
Log fold change on Limma
limma multiple factor design
updated 6.9 years ago by 13k • written 6.9 years ago by ▴ 20
11
votes
9
replies
1.1k
views
Correlation of a Linear Variable
limma limma design matrix
updated 7.2 years ago by 60k • written 7.2 years ago by ▴ 360
11
votes
9
replies
2.4k
views
How to remove more than two batches in my data-sets
limma RNAseq removebatcheffect()
updated 5.9 years ago by 45k • written 5.9 years ago by ▴ 30
11
votes
3
replies
1.1k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 5.8 years ago by ★ 2.9k • written 5.8 years ago by ▴ 100
11
votes
5
replies
10k
views
Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 4.8 years ago by 45k • written 13.5 years ago by ▴ 190
10
votes
13
replies
3.2k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R limma oligo differential gene expression affymetrix microarrays
updated 6.9 years ago by • 0 • written 6.9 years ago by ▴ 10
10
votes
14
replies
2.5k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 70
10
votes
8
replies
5.8k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 60
10
votes
11
replies
5.2k
views
Standard error and effect size from Limma
effect size Limma toptable Standard Error
updated 6.9 years ago by 45k • written 6.9 years ago by ▴ 20
10
votes
13
replies
2.2k
views
DE for genes with very low counts using limma.
limma voom limma-trend
updated 5.6 years ago by 45k • written 5.6 years ago by ▴ 140
10
votes
4
replies
1.8k
views
Adjust for multiple batches using combat
combat sva limma
updated 5.2 years ago by ★ 27k • written 5.2 years ago by • 0
10
votes
6
replies
8.1k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 6.6 years ago by ▴ 610 • written 6.6 years ago by ▴ 100
50 results • Page 1 of 1
Recent ...
Replies
Comment: Italicise by Pau • 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa by priyanka.m • 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values by wahaha • 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Comment: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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