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Answer: Answer: Limma-voom sample weights and impact on DEG numbers
6 days ago Gordon Smyth 53k
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198
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Comment: Comment: segfault in edgeR glmQLFit
7 days ago Gordon Smyth 53k
0
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1
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198
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Answer: Answer: segfault in edgeR glmQLFit
10 days ago • updated 9 days ago Gordon Smyth 53k
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285
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Comment: Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
10 days ago Gordon Smyth 53k
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285
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Answer: Answer: How does contrasts.fit do in limma to extract comparisons with a model having in
11 days ago Gordon Smyth 53k
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188
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Answer: Answer: PTM analysis in LIMPA
25 days ago Gordon Smyth 53k
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1.3k
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Answer: Answer: two questions about limma
4 weeks ago Gordon Smyth 53k
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0
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413
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Comment: Comment: Large logFC but somewhat high FDR
5 weeks ago Gordon Smyth 53k
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1
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1.3k
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Answer: Answer: p.adjust BH Question
5 weeks ago Gordon Smyth 53k
1
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1
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413
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Answer: Answer: Large logFC but somewhat high FDR
5 weeks ago Gordon Smyth 53k
0
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1
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188
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Answer: Answer: limpa - drivers for unusually high standard error?
5 weeks ago Gordon Smyth 53k
2
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1
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284
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Answer: Answer: Identifying differentially expressed genes in individual samples from a large co
5 weeks ago Gordon Smyth 53k
2
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216
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Answer: Answer: Post translational modifications and phosphoproteomics in limpa?
6 weeks ago Gordon Smyth 53k
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233
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Answer: Answer: How to model DE for RNA-seq in concordant monozygotic twins?
12 weeks ago Gordon Smyth 53k
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0
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400
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Comment: Comment: incomplete imputation of missing values with LEA impute() function
12 weeks ago Gordon Smyth 53k
0
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1
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440
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Answer: Answer: Help with defining groups
3 months ago Gordon Smyth 53k
0
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0
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1.3k
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Comment: Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
3 months ago Gordon Smyth 53k
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1
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1.3k
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Comment: Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
3 months ago Gordon Smyth 53k
2
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321
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Answer: Answer: replace cat with message in glmTreat when lfc = 0
3 months ago Gordon Smyth 53k
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1
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1.3k
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Comment: Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
3 months ago Gordon Smyth 53k
2
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1
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1.3k
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Comment: Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
3 months ago Gordon Smyth 53k
3
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2
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1.3k
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Answer: Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
3 months ago Gordon Smyth 53k
0
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0
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455
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Comment: Comment: voomLmFit fitted log-CPM values
3 months ago Gordon Smyth 53k
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1
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455
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Answer: Answer: voomLmFit fitted log-CPM values
3 months ago Gordon Smyth 53k
0
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0
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387
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Comment: Comment: ROAST compare results with complex design
3 months ago Gordon Smyth 53k
0
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0
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770
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Comment: Comment: Are voomByGroup and voomLmFit compatible?
4 months ago • updated 3 months ago Gordon Smyth 53k
1
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0
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770
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Comment: Comment: Are voomByGroup and voomLmFit compatible?
4 months ago Gordon Smyth 53k
1
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1
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563
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Comment: Comment: p-adjusted values in multiple comparisons
4 months ago Gordon Smyth 53k
0
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1
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770
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Comment: Comment: Are voomByGroup and voomLmFit compatible?
4 months ago Gordon Smyth 53k
2
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1
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563
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Answer: Answer: p-adjusted values in multiple comparisons
4 months ago Gordon Smyth 53k
1
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2
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770
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Answer: Answer: Are voomByGroup and voomLmFit compatible?
4 months ago Gordon Smyth 53k
1
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0
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370
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Answer: Answer: Can limma be used with module eigengenes instead of genes?
4 months ago Gordon Smyth 53k
1
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0
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1.0k
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Comment: Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
4 months ago Gordon Smyth 53k
0
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1
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1.0k
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Comment: Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
4 months ago Gordon Smyth 53k
1
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0
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384
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Answer: Answer: Testing KO vs WT at day4/day14 with interactions in edgeR
4 months ago Gordon Smyth 53k
1
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1
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1.0k
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Answer: Answer: Transcript expression analysis in edgeR from gtf file obtained from merging long
4 months ago Gordon Smyth 53k
0
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1
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1.0k
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Comment: Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
4 months ago Gordon Smyth 53k
0
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1
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1.0k
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Comment: Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long
4 months ago Gordon Smyth 53k
1
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1
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402
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Answer: Answer: Difference between logFC in limma-voom and weighted limma-voom
4 months ago Gordon Smyth 53k
3
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0
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400
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Answer: Answer: Limpa Pipeline Order
4 months ago Gordon Smyth 53k
3
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1
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474
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Answer: Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
4 months ago Gordon Smyth 53k
2
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1
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441
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Answer: Answer: Limma : paired samples leading to unexpected estimates
5 months ago Gordon Smyth 53k
2
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1
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543
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Answer: Answer: (Why) do limma's confidence intervals depend on topTable's p.value argument?
5 months ago Gordon Smyth 53k
0
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0
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1.9k
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Comment: Comment: weird model design for DE analysis
5 months ago Gordon Smyth 53k
2
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1
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937
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Answer: Answer: Transcript expression analysis using EdgeR
5 months ago Gordon Smyth 53k
0
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0
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959
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Answer: Answer: Using offset in edgeR
5 months ago Gordon Smyth 53k
1
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1
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2.5k
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Answer: Answer: Non-monotonic voomByGroup plot in Xenium data
5 months ago Gordon Smyth 53k
1
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1
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2.0k
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Answer: Answer: Should Xenium pseudobulk experiments be analysed like microarrays (limma) or lik
5 months ago Gordon Smyth 53k
2
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0
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5.7k
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Comment: Comment: competitive enrichment test yields too few significant results, self-contained t
5 months ago Gordon Smyth 53k
1
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1
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5.7k
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Comment: Comment: competitive enrichment test yields too few significant results, self-contained t
5 months ago Gordon Smyth 53k
5,313 results • Page 1 of 107
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