Showing : DE • reset
0
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2
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Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 8.3 years ago by 42k • written 8.3 years ago by • 0
2
votes
5
replies
3.2k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect limma rna seq DE
updated 4.0 years ago by ★ 13k • written 4.0 years ago by ▴ 830
2
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2
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2.7k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
5
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7
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2.2k
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 4.1 years ago by 50k • written 4.1 years ago by ▴ 60
3
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5
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2.1k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 4.1 years ago by 42k • written 4.1 years ago by ▴ 830
6
votes
6
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2.0k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 4.1 years ago by 50k • written 4.1 years ago by ▴ 60
2
votes
7
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2.0k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
7
votes
13
replies
1.9k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 5.3 years ago by ★ 7.9k • written 5.3 years ago by ▴ 830
1
vote
5
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1.7k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
0
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5
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1.7k
views
DESeq2 for DE analysis in developmental stages of tomato pollen
DESeq2 DE normalization
6.8 years ago mario.keller.1988 ▴ 20
1
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2
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1.7k
views
Error message running DE-test in Monocle
monocle cummerbund DE rnaseq
updated 8.8 years ago by • 0 • written 9.1 years ago by ▴ 250
3
votes
3
replies
1.4k
views
Different number of marker genes between same clusters
sce markers single cell DE clusters
4.6 years ago ludmi.b • 0
3
votes
4
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1.3k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 10
3
votes
5
replies
1.3k
views
Different numbers of DE genes using edgeR and DESEQ2
edger deseq2 rnaseq de
updated 4.1 years ago by 50k • written 4.1 years ago by ▴ 60
0
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2
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1.2k
views
coef for limma differential expression analysis
limma DE
updated 7.2 years ago by ▴ 830 • written 7.2 years ago by • 0
0
votes
3
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1.0k
views
DESeq2 - nested samples (individuals) - time course - conditions
deseq2 nested de
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
0
votes
1
reply
952
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
1
reply
920
views
Multi-level experiment with continuous varibles and confounders in limma
limma de differential gene expression multi-tissue design multi-level design
updated 4.1 years ago by ★ 28k • written 4.1 years ago by • 0
1
vote
1
reply
642
views
different observation of DEG for same group
deseq2 DE
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
19 results • Page 1 of 1
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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