Showing : differential gene expression • reset
7
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9
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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
1
vote
10
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6.4k
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DESEQ2: apparently wrong log2(fold-change) calculation
deseq2 differential gene expression log2fc
9.0 years ago Osvaldo ▴ 40
9
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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
1
vote
6
replies
1.4k
views
design of edgeR GLM test
edger differential gene expression glmlrt()
8.3 years ago • updated 8.2 years ago simarsidhu25 • 0
0
votes
7
replies
2.4k
views
DESeq2 with interest only for 1 gene
R deseq2 differential gene expression help
8.7 years ago fischer87 • 0
20
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18
replies
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
5
votes
9
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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
2
votes
6
replies
2.0k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast limma pathway analysis differential gene expression affymetrix
10.0 years ago svlachavas ▴ 840
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
4
votes
6
replies
1.7k
views
Differential expression across gene features
limma deseq2 differential gene expression
written 8.9 years ago by ▴ 90
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
2
votes
5
replies
4.4k
views
processing data with 2 rep or one replicate by ballgown
ballgown differential gene expression
updated 8.4 years ago by ▴ 210 • written 8.4 years ago by • 0
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
3
votes
6
replies
2.7k
views
Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix toptable makecontrasts differential gene expression
7.5 years ago stinehedensted • 0
4
votes
4
replies
2.0k
views
Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
edger differential gene expression upregulated genes downregulated genes
updated 6.9 years ago by • 0 • written 6.9 years ago by ▴ 60
2
votes
9
replies
6.5k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.0 years ago by ▴ 10
0
votes
8
replies
3.2k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
9.3 years ago • updated 9.2 years ago newsomew13 • 0
3
votes
12
replies
26k
views
P Value of 0?
differential gene expression edger
updated 10.1 years ago by ▴ 180 • written 10.1 years ago by • 0
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
3
votes
6
replies
2.8k
views
How to get a list of differentialy expressed genes with data from Illumina array?
limma illumina microarray lmfit differential gene expression
updated 9.6 years ago by 68k • written 9.6 years ago by ▴ 10
1
vote
3
replies
1.7k
views
WGCNA Co-expression
microarray differential gene expression module
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by • 0
1
vote
4
replies
2.1k
views
Selection of appropriate gene filtering method for discovering statistically significant genes for Affymetrix arrays
bioconductor differential gene expression independent filtering
10.2 years ago svlachavas ▴ 840
2
votes
5
replies
1.8k
views
DESeq2 problem with outlier replacement in paired multi-factor design
deseq2 differential gene expression multiple factor design paired design
8.2 years ago • updated 8.1 years ago gregory.l.stone ▴ 10
10
votes
4
replies
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
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
3
votes
6
replies
2.2k
views
Clarification MAplot and FDR in EdgeR
edgeR MAplot rnaseq differential gene expression
updated 8.6 years ago by 52k • written 8.6 years ago by • 0
0
votes
2
replies
3.2k
views
DESeq2 different results from similar datasets
deseq2 differential gene expression rna-seq
9.3 years ago erin.gill81 ▴ 60
0
votes
2
replies
3.3k
views
Use surrogate variables on DESeq2
deseq2 sva deseq differential gene expression
updated 8.8 years ago by ▴ 20 • written 9.6 years ago by ▴ 40
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
3
votes
3
replies
1.3k
views
how to perform a Differential gene expression when you don't have any reference matrix?
microarray gene regulated differential gene expression
10.1 years ago Nemo ▴ 80
1
vote
2
replies
1.5k
views
Deseq2 analysis with replicates only for control
deseq2 differential gene expression
updated 9.4 years ago by 43k • written 9.4 years ago by ▴ 20
1
vote
7
replies
6.4k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 8.1 years ago by ★ 3.6k • written 8.1 years ago by ▴ 10
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
2
votes
5
replies
3.4k
views
Programs used in RNA-seq workflow
deseq2 bioconductor workflows differential gene expression rnaseqgene
9.0 years ago cirisarri95 • 0
2
votes
4
replies
1.6k
views
Interprentation of appropriate statistical test
samr SAM siggenes bioconductor differential gene expression
10.1 years ago svlachavas ▴ 840
3
votes
13
replies
2.7k
views
Design and independent filtering of patient RNA-seq data
differential gene expression deseq2 design independent filtering limma
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 110
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
1
vote
7
replies
2.7k
views
CellCODE not installing
differential gene expression microarray
9.0 years ago christopher.clarskon15 ▴ 20
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
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
0
votes
3
replies
1.3k
views
detect cancer in some tissue
cancer differential gene expression
updated 9.2 years ago by ▴ 10 • written 9.3 years ago by • 0
3
votes
2
replies
5.9k
views
DESEQ2 Experimental Design
deseq2 differential gene expression
10.1 years ago fabiola • 0
0
votes
2
replies
2.9k
views
Remove batch effect - condition partially confounded by data
combat differential gene expression sva
updated 10.2 years ago by ▴ 650 • written 10.2 years ago by • 0
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
1
vote
2
replies
1.8k
views
Question about read.maimages
differential gene expression limma read.maimages
updated 9.9 years ago by 52k • written 9.9 years ago by ▴ 10
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
1
vote
4
replies
1.6k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
9.4 years ago arrigonialberto86 • 0
0
votes
2
replies
3.8k
views
Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 7.0 years ago by • 0 • written 9.9 years ago by • 0
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
4
votes
8
replies
3.1k
views
Can't find any differentially expressed genes
rnaseq differential gene expression design matrix edgeR
updated 9.9 years ago by 52k • written 10.0 years ago by ▴ 10
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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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