Showing : limma • reset
32
votes
10
replies
38k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
updated 12 months ago by • 0 • written 10.4 years ago by ▴ 250
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
28
votes
8
replies
12k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 6.6 years ago by 50k • written 9.1 years ago by ▴ 150
25
votes
9
replies
6.8k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 9.2 years ago by 50k • written 9.2 years ago by ▴ 40
24
votes
12
replies
12k
views
Nanostring analysis with limma
nanostring limma
updated 9.0 years ago by ▴ 20 • written 9.0 years ago by ▴ 370
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 8.2 years ago by 50k • written 8.2 years ago by ▴ 50
22
votes
8
replies
4.1k
views
Limma camera function never gives any differentially expressed gene sets
limma
updated 6.7 years ago by • 0 • written 8.8 years ago by ▴ 420
22
votes
4
replies
9.9k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 8.9 years ago by 50k • written 8.9 years ago by ▴ 830
21
votes
5
replies
14k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 9.0 years ago by 50k • written 9.9 years ago by ▴ 190
21
votes
7
replies
9.5k
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 50k • written 6.6 years ago by • 0
19
votes
10
replies
4.1k
views
Do the outputs of Limma's competitive gene set methods (camera, romer) require a mutliple testing correction?
limma romer
updated 8.7 years ago by 50k • written 8.7 years ago by ▴ 40
18
votes
3
replies
2.9k
views
cameraPR vs geneSetTest and ROAST/CAMERA in general
limma voomwithqualityweights gene set analysis
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 80
18
votes
18
replies
4.8k
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 8.6 years ago by ▴ 850 • written 8.6 years ago by ▴ 830
18
votes
37
replies
16k
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
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 • 0 • written 6.8 years ago by ▴ 20
17
votes
5
replies
4.7k
views
limma voom Mean-variance trend plot: x-axis?
limma
5.0 years ago AS ▴ 70
17
votes
7
replies
5.9k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7.9 years ago by ★ 7.9k • written 7.9 years ago by ▴ 10
16
votes
5
replies
7.4k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 8.4 years ago by 50k • written 8.4 years ago by ▴ 120
16
votes
0
replies
3.7k
views
simultaneous use of robust and weighting methods in limma
limma robust arrayWeights
10.4 years ago • updated 7.9 years ago Gordon Smyth 50k
16
votes
13
replies
4.3k
views
Camera and ROAST
limma
updated 6.4 years ago by 50k • written 6.4 years ago by ▴ 30
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 4 days ago Chris • 0
15
votes
6
replies
3.2k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 7.7 years ago by ▴ 90 • written 7.7 years ago by ▴ 170
15
votes
14
replies
3.6k
views
extract similar expressed genes (SEGs) rather than DEGs
limma microarray
updated 9.2 years ago by 21k • written 9.3 years ago by ▴ 340
15
votes
4
replies
2.7k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by ▴ 130
14
votes
16
replies
2.6k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 8.8 years ago by 65k • written 8.8 years ago by ▴ 10
14
votes
9
replies
3.7k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 6.3 years ago by ▴ 130 • written 8.0 years ago by ▴ 80
14
votes
16
replies
2.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
7.9 years ago giroudpaul ▴ 40
14
votes
12
replies
9.3k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 7.7 years ago by ★ 13k • written 7.7 years ago by ▴ 30
13
votes
2
replies
3.1k
views
voom with combat
limma voom combat batch effect
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 10
13
votes
6
replies
6.2k
views
goana limma- extract list of DE genes and genes in the enriched GO terms?
limma goana
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 20
13
votes
3
replies
12k
views
Understanding contrasts limma
limma design and contrast matrix
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 60
13
votes
21
replies
6.0k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma voom hurdle single cell
8.6 years ago osa.zuta ▴ 40
13
votes
2
replies
6.4k
views
Using limma when continuous and categorical confounders are present at the same time (e.g.age, gender)
limma covariate continuous categorical adjustment
updated 8.8 years ago by 50k • written 8.8 years ago by • 0
12
votes
6
replies
1.6k
views
Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
12
votes
12
replies
749
views
Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by ★ 3.3k • written 4 days ago by • 0
12
votes
4
replies
4.4k
views
differential expression analysis of htseq data with edgeR/voom
voom htseq edgeR limma RNASeq123
updated 5.3 years ago by 50k • written 6.9 years ago by ▴ 30
12
votes
9
replies
7.9k
views
Appropriate use of the function treat of the limma package
limma treat microarray bioconductor
9.1 years ago svlachavas ▴ 830
12
votes
9
replies
3.2k
views
Limma residuals matrix
limma
updated 4.7 years ago by 50k • written 4.7 years ago by ▴ 20
12
votes
20
replies
2.0k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 8.6 years ago by ★ 28k • written 8.7 years ago by ▴ 830
11
votes
6
replies
3.7k
views
Log fold change on Limma
limma multiple factor design
updated 8.8 years ago by ★ 13k • written 8.8 years ago by ▴ 20
11
votes
9
replies
1.6k
views
Correlation of a Linear Variable
limma limma design matrix
updated 9.1 years ago by 65k • written 9.1 years ago by ▴ 370
11
votes
8
replies
10k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 80
11
votes
9
replies
4.4k
views
How to remove more than two batches in my data-sets
limma RNAseq removebatcheffect()
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 30
11
votes
4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.2 years ago by • 0
11
votes
16
replies
1.8k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma multifactorial design diagnostic plots affymetrix microarrays
updated 8.6 years ago by 65k • written 8.6 years ago by ▴ 830
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 50k • written 15.4 years ago by ▴ 190
11
votes
3
replies
1.7k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.8 years ago by ★ 3.3k • written 7.8 years ago by ▴ 110
11
votes
18
replies
4.8k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 3.1 years ago by 50k • written 3.6 years ago by ▴ 10
10
votes
3
replies
9.0k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot limma fdr
6.8 years ago • updated 3.4 years ago tcalvo ▴ 90
10
votes
4
replies
2.9k
views
Adjust for multiple batches using combat
combat sva limma
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
50 results • Page 1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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