Showing : differential gene expression • reset
20
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18
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5.6k
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 9.5 years ago by ▴ 870 • written 9.5 years ago by ▴ 840
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
9.8 years ago • updated 9.7 years ago svlachavas ▴ 840
17
votes
14
replies
49k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 2.7 years ago by • 0 • written 7.7 years ago by ▴ 20
14
votes
16
replies
3.2k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 9.7 years ago by 68k • written 9.7 years ago by ▴ 10
12
votes
6
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3.1k
views
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger differential gene expression rnaseq
updated 8.0 years ago by 52k • written 8.0 years ago by ▴ 20
12
votes
6
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1.8k
views
Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 10
11
votes
8
replies
12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 80
10
votes
4
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5.2k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 8.6 years ago by 52k • written 8.6 years ago by ▴ 110
10
votes
14
replies
14k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 4.0 years ago by ▴ 20 • written 9.1 years ago by ▴ 30
10
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13
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5.0k
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 9.7 years ago by • 0 • written 9.7 years ago by ▴ 10
9
votes
10
replies
5.5k
views
Simple significance test functions from R packages limma and plsgenomics
limma plsgenomics microarray differential gene expression
updated 10.2 years ago by 52k • written 10.2 years ago by ▴ 10
9
votes
5
replies
5.7k
views
Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 6.4 years ago by ★ 13k • written 6.4 years ago by • 0
8
votes
7
replies
2.4k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 5.7 years ago by • 0 • written 6.5 years ago by ▴ 20
8
votes
2
replies
2.8k
views
limma-voom when testing differential expression of a subset of genes.
limma voom differential gene expression
updated 9.7 years ago by 52k • written 9.7 years ago by ▴ 40
7
votes
9
replies
5.7k
views
LIMMA: interpreting interaction terms in an unbalanced factorial design with repeated measures
LIMMA FACTORIAL REPEATED MEASURES differential gene expression
9.6 years ago • updated 9.4 years ago robert.maughan • 0
7
votes
8
replies
6.3k
views
Only one replicate: inferring dispersion from other group
deseq2 edger limma differential gene expression
updated 10.3 years ago by 52k • written 10.3 years ago by ▴ 30
7
votes
7
replies
3.5k
views
Using Sailfish estimated read-counts for DESeq2 analysis
deseq2 sailfish differential gene expression
updated 10.3 years ago by ★ 3.8k • written 10.3 years ago by • 0
7
votes
6
replies
6.8k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 60
7
votes
18
replies
4.3k
views
RNA-seq analysis using EdgeR- I need to make sure that the codes that I use to analyze the data are correct
rnaseq edger differential gene expression
updated 9.0 years ago by ★ 7.9k • written 9.0 years ago by • 0
6
votes
4
replies
4.4k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 9.7 years ago by ★ 28k • written 9.7 years ago by ▴ 840
6
votes
19
replies
4.5k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 7.5 years ago by ▴ 690 • written 7.5 years ago by ▴ 50
6
votes
12
replies
19k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
6
votes
13
replies
3.8k
views
DEseq2 with limited gene set
DEseq2 differential gene expression
8.6 years ago dmr210 • 0
6
votes
10
replies
2.2k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing roast mroast differential gene expression bioconductor
9.8 years ago svlachavas ▴ 840
6
votes
12
replies
5.8k
views
DESEq2 - Why is "my gene" not differentially expressed?
deseq2 differential gene expression
9.0 years ago Jane Merlevede ▴ 90
6
votes
7
replies
2.6k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
5
votes
6
replies
3.7k
views
Differential expression analysis - additive genetic model (how to implement it)
deseq2 edger differential gene expression additive model
9.3 years ago • updated 9.2 years ago jlerga • 0
5
votes
2
replies
4.5k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 3.0 years ago by • 0 • written 7.5 years ago by • 0
5
votes
9
replies
3.7k
views
Merge different datasets regarding a common number of DE genes in R
bioconductor expresiondataset affymetrixchip differential gene expression
10.0 years ago svlachavas ▴ 840
5
votes
4
replies
1.8k
views
How to remove dublicate probesets matching to the same gene, after toptable in order to have a genelist without dublicate gene Symbols for further GO…
bioconductor limma differential gene expression dublicate
10.1 years ago svlachavas ▴ 840
5
votes
6
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1.7k
views
Confusing: identify differentially expression genes (DEG) perturbed by a drug in Limma
limma cmap microarrays differential gene expression
8.2 years ago • updated 8.1 years ago kevin.m.hao ▴ 10
5
votes
6
replies
1.9k
views
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
5
votes
3
replies
1.8k
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
6.1 years ago S.Webb6 ▴ 40
5
votes
4
replies
3.2k
views
Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 3.8 years ago by 52k • written 6.8 years ago by ▴ 120
5
votes
5
replies
2.9k
views
Performing differential gene analysis on RT PCR experimental data
differential gene expression
updated 7.1 years ago by 52k • written 7.1 years ago by ▴ 10
5
votes
1
reply
2.1k
views
WGCNA - looking for over-representation of DEGs within gene networks
wgcna r differential gene expression bioconductor
updated 9.2 years ago by ★ 3.0k • written 9.2 years ago by ▴ 30
5
votes
12
replies
5.6k
views
Differential expression analysis: comparison of DESeq2 and edgeR robust results
deseq2 edgeR differential gene expression
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 90
5
votes
12
replies
8.3k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 6.9 years ago by 52k • written 6.9 years ago by ▴ 120
5
votes
14
replies
6.2k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 2.9 years ago by ★ 4.7k • written 6.7 years ago by ▴ 60
4
votes
4
replies
2.0k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
4
votes
7
replies
2.0k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 8.7 years ago by 68k • written 8.7 years ago by ★ 1.5k
4
votes
4
replies
3.0k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
4
votes
4
replies
2.9k
views
Non-specific filtering methodogies for ExpressionSet in R/Bioconductor
genefilter R bioconductor differential gene expression
updated 10.2 years ago by 52k • written 10.2 years ago by ▴ 840
4
votes
2
replies
1.5k
views
limma; Only fit list of certain genes/ filter eSet
limma filter genelist differential gene expression
updated 8.4 years ago by 52k • written 8.4 years ago by • 0
4
votes
7
replies
3.3k
views
Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
edger differential gene expression glmlrt()
8.3 years ago simarsidhu25 • 0
4
votes
6
replies
3.6k
views
edgeR on DEG analysis: Size cannot be NA nor exceed 65536
edger differential gene expression
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
4
votes
1
reply
2.2k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
7.6 years ago Andrew_McDavid ▴ 270
4
votes
2
replies
1.4k
views
Differential gene expression for multi-factorial experiment using edgeR
edger differential gene expression multiple factor design
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
4
votes
1
reply
1.6k
views
tests for equivalence with LIMMA
limma differential gene expression equivalence TOST DOSTT
updated 10.1 years ago by 68k • written 10.1 years ago by ▴ 340
4
votes
6
replies
1.7k
views
Differential expression across gene features
limma deseq2 differential gene expression
written 8.9 years ago by ▴ 90
50 results • Page 1 of 1
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Comment: Problem at champ.load by Josh • 0
See my anser--I was able to fix this error by installing a specific ChAMP version
Answer: Problem at champ.load by Josh • 0
It looks like the current Bioconducter version of ChAMP (2.36) does not support EPICv2. You have to install a github version of a previous …
Comment: DESeq2 model - How to test case/control time course model when taking account wi by wuwenhui2 • 0
@mikelove Dear Dr. Love, for this design, you recommend using the model "~condition + time + condition:subject.nested + condition:time" com…
Answer: myvariant error by Christelle • 0
An example of my data : [1] "chr1:g.877831T>C" [2] "chr1:g.878314G>C" …
Comment: Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Ana by ATpoint ★ 4.7k
Why was my comment removed? It's irritating that it was moderated away without leaving any note.
Votes
Comment: Identifying potentially associated gene set to drug response using GSVA
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
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