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Comment: Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
5 months ago Gordon Smyth 53k
2
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Answer: Answer: replace cat with message in glmTreat when lfc = 0
5 months ago Gordon Smyth 53k
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Comment: Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
5 months ago Gordon Smyth 53k
2
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1
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1.8k
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Comment: Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
5 months ago Gordon Smyth 53k
3
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2
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1.8k
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Answer: Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
5 months ago Gordon Smyth 53k
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548
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Comment: Comment: voomLmFit fitted log-CPM values
5 months ago Gordon Smyth 53k
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548
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Answer: Answer: voomLmFit fitted log-CPM values
5 months ago Gordon Smyth 53k
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459
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Comment: Comment: ROAST compare results with complex design
5 months ago Gordon Smyth 53k
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859
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Comment: Comment: Are voomByGroup and voomLmFit compatible?
6 months ago • updated 5 months ago Gordon Smyth 53k
1
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859
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Comment: Comment: Are voomByGroup and voomLmFit compatible?
6 months ago Gordon Smyth 53k
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695
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Comment: Comment: p-adjusted values in multiple comparisons
6 months ago Gordon Smyth 53k
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859
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Comment: Comment: Are voomByGroup and voomLmFit compatible?
6 months ago Gordon Smyth 53k
2
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1
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695
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Answer: Answer: p-adjusted values in multiple comparisons
6 months ago Gordon Smyth 53k
1
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2
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859
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Answer: Answer: Are voomByGroup and voomLmFit compatible?
6 months ago Gordon Smyth 53k
1
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0
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446
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Answer: Answer: Can limma be used with module eigengenes instead of genes?
6 months ago Gordon Smyth 53k
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1.2k
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Comment: Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
6 months ago Gordon Smyth 53k
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1
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1.2k
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Comment: Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
6 months ago Gordon Smyth 53k
1
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0
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471
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Answer: Answer: Testing KO vs WT at day4/day14 with interactions in edgeR
6 months ago Gordon Smyth 53k
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1.2k
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Answer: Answer: Transcript expression analysis in edgeR from gtf file obtained from merging long
6 months ago Gordon Smyth 53k
0
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1
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1.2k
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Comment: Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
6 months ago Gordon Smyth 53k
0
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1
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1.2k
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Comment: Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
6 months ago Gordon Smyth 53k
1
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1
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464
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Answer: Answer: Difference between logFC in limma-voom and weighted limma-voom
6 months ago Gordon Smyth 53k
3
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572
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Answer: Answer: Limpa Pipeline Order
6 months ago Gordon Smyth 53k
3
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1
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530
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Answer: Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
6 months ago Gordon Smyth 53k
2
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1
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528
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Answer: Answer: Limma : paired samples leading to unexpected estimates
7 months ago Gordon Smyth 53k
2
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1
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675
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Answer: Answer: (Why) do limma's confidence intervals depend on topTable's p.value argument?
7 months ago Gordon Smyth 53k
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2.0k
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Comment: Comment: weird model design for DE analysis
7 months ago Gordon Smyth 53k
2
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1
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1.2k
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Answer: Answer: Transcript expression analysis using EdgeR
7 months ago Gordon Smyth 53k
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0
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1.1k
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Answer: Answer: Using offset in edgeR
7 months ago Gordon Smyth 53k
1
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1
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2.6k
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Answer: Answer: Non-monotonic voomByGroup plot in Xenium data
7 months ago Gordon Smyth 53k
1
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1
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2.2k
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Answer: Answer: Should Xenium pseudobulk experiments be analysed like microarrays (limma) or lik
7 months ago Gordon Smyth 53k
2
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0
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5.9k
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Comment: Comment: competitive enrichment test yields too few significant results, self-contained t
7 months ago Gordon Smyth 53k
1
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1
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5.9k
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Comment: Comment: competitive enrichment test yields too few significant results, self-contained t
7 months ago Gordon Smyth 53k
2
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1
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5.9k
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Answer: Answer: competitive enrichment test yields too few significant results, self-contained t
7 months ago Gordon Smyth 53k
0
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0
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1.5k
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Answer: Answer: How to avoid losing a sample as reference running an individual differential exp
7 months ago Gordon Smyth 53k
0
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0
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2.6k
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Comment: Comment: Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-
7 months ago Gordon Smyth 53k
0
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1
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3.5k
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Comment: Comment: I would like to perform differential expression analysis of lncRNAs using DESeq2
8 months ago Gordon Smyth 53k
0
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1
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2.6k
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Answer: Answer: Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-
8 months ago • updated 7 months ago Gordon Smyth 53k
1
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1
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3.5k
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Answer: Answer: I would like to perform differential expression analysis of lncRNAs using DESeq2
8 months ago Gordon Smyth 53k
1
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1
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3.9k
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Answer: Answer: Is voomByGroup available in limma?
8 months ago Gordon Smyth 53k
0
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1
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1.9k
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Answer: Answer: How to use goana function with zebrafish genome from org.Dr.eg.db
8 months ago Gordon Smyth 53k
0
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1
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1.9k
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Comment: Comment: How to use goana function with zebrafish genome from org.Dr.eg.db
8 months ago Gordon Smyth 53k
0
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0
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420
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Job: Lab Head positions at the WEHI, Melbourne, Australia
JobPosting Bioconductor
8 months ago Gordon Smyth 53k
3
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1
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6.5k
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Answer: Answer: limma duplicateCorrelation appropriate where some blocks cross condition and som
9 months ago Gordon Smyth 53k
1
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1
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2.8k
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Comment: Comment: Altered (negative or positive) logFC values for same gene from two intitial coun
9 months ago Gordon Smyth 53k
1
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1
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2.8k
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Answer: Answer: Altered (negative or positive) logFC values for same gene from two intitial coun
9 months ago Gordon Smyth 53k
0
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0
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1.7k
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Comment: Comment: Differential gene expression analysis on haplotype-resolved diploid assembly
9 months ago Gordon Smyth 53k
2
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1
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1.7k
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Answer: Answer: Differential gene expression analysis on haplotype-resolved diploid assembly
9 months ago Gordon Smyth 53k
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1
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4.3k
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Comment: Comment: parameters of filterByExpr
9 months ago Gordon Smyth 53k
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0
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1.0k
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Answer: Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi
9 months ago Gordon Smyth 53k
5,346 results • Page 2 of 107
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