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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
8.3 years ago Aaron Lun ★ 29k
12
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Answer: A: LogFC: how do you determine the cutoff for differentially expressed genes?
8.3 years ago Aaron Lun ★ 29k
7
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2
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1.8k
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Duplicated author affiliations in BiocStyle-based HTML document
biocstyle vignette
updated 8.3 years ago by ▴ 750 • written 8.4 years ago by ★ 29k
1
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Comment: C: edgeR and lack of counts ID on CPM matrix
8.3 years ago Aaron Lun ★ 29k
2
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1
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4.0k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
8.3 years ago Aaron Lun ★ 29k
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0
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2.3k
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Answer: A: edgeR and lack of counts ID on CPM matrix
8.3 years ago Aaron Lun ★ 29k
1
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1
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4.0k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
8.3 years ago Aaron Lun ★ 29k
0
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0
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4.0k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
8.3 years ago Aaron Lun ★ 29k
0
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1
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4.0k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
8.3 years ago Aaron Lun ★ 29k
0
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1
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4.0k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
8.3 years ago Aaron Lun ★ 29k
0
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1
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4.0k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
8.3 years ago Aaron Lun ★ 29k
0
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0
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2.2k
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Comment: C: EdgeR model not of full rank
8.3 years ago Aaron Lun ★ 29k
1
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2
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2.9k
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Comment: C: Multi-level experiment with limma
8.3 years ago Aaron Lun ★ 29k
5
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1
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2.9k
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Answer: A: Multi-level experiment with limma
8.3 years ago Aaron Lun ★ 29k
0
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1
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3.3k
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Comment: C: How does newSCESet calculate expression matrix
8.4 years ago Aaron Lun ★ 29k
0
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0
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1.4k
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Comment: C: Adjusting for procedural effect
8.4 years ago Aaron Lun ★ 29k
1
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1
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1.4k
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Answer: A: Is bioconductor a good platform for what I am thinking of
8.4 years ago Aaron Lun ★ 29k
2
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0
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1.4k
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Answer: A: Adjusting for procedural effect
8.4 years ago Aaron Lun ★ 29k
0
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1
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2.7k
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Comment: C: Adjusting for procedural effect and deciding on statistical test
8.4 years ago Aaron Lun ★ 29k
1
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1
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1.9k
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Answer: A: Limma validity for only hundreds of genes/metabolites
8.4 years ago Aaron Lun ★ 29k
3
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0
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6.7k
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Answer: A: Cell type specific cell markers for Seurat based analysis.
8.4 years ago Aaron Lun ★ 29k
0
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1
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2.2k
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Answer: A: EdgeR model not of full tank
8.4 years ago Aaron Lun ★ 29k
0
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0
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1.9k
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Comment: C: Accounting for both categorical and numerical possible confounding variables in
8.4 years ago Aaron Lun ★ 29k
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624
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Answer: A: Error message when trying to access packages
8.4 years ago Aaron Lun ★ 29k
0
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1
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2.7k
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Comment: C: Adjusting for procedural effect and deciding on statistical test
8.4 years ago Aaron Lun ★ 29k
3
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0
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1.5k
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Answer: A: Normalizing vs RNA content in scRNAseq data
8.4 years ago Aaron Lun ★ 29k
1
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1.3k
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Answer: A: cydar: negative values for cell assignment indices
8.4 years ago Aaron Lun ★ 29k
3
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0
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1.9k
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Answer: A: Accounting for both categorical and numerical possible confounding variables in
8.4 years ago Aaron Lun ★ 29k
0
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0
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3.5k
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Comment: C: Help with design matrix for two cell types, multiple treatments
8.4 years ago Aaron Lun ★ 29k
0
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0
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1.6k
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Comment: C: Limma: model Design matrix and contrast matrix for getting gene log2 fold change
8.4 years ago Aaron Lun ★ 29k
1
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0
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1.8k
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Answer: A: accounting for phylogenetic non-independence in differential expression analysis
8.4 years ago Aaron Lun ★ 29k
0
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0
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2.8k
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Comment: C: Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma
8.4 years ago Aaron Lun ★ 29k
0
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1
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2.8k
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Comment: C: Three way-interaction on voom (limma) data, including a factor with > 2 levels
8.4 years ago Aaron Lun ★ 29k
2
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2
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2.8k
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Answer: A: Three way-interaction on voom (limma) data, including a factor with > 2 levels
8.4 years ago Aaron Lun ★ 29k
5
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2
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2.8k
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Answer: A: Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma
8.4 years ago Aaron Lun ★ 29k
0
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1
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22k
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Comment: C: DESeq2 for ChIP-seq differential peaks
8.4 years ago Aaron Lun ★ 29k
1
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0
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3.2k
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Answer: A: Best way to get HiCUP-mapped Hi-C data into diffHiC
8.4 years ago Aaron Lun ★ 29k
2
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1
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695
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Answer: A: using edgeR or limma for 5C data normalization
8.4 years ago Aaron Lun ★ 29k
1
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1
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1.6k
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Answer: A: Limma: model Design matrix and contrast matrix for getting gene log2 fold change
8.4 years ago Aaron Lun ★ 29k
5
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0
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2.1k
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Answer: A: Intercept in design matrix
8.4 years ago Aaron Lun ★ 29k
0
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0
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1.5k
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Answer: A: EdgeR dispersion and FDR
8.4 years ago Aaron Lun ★ 29k
2
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1
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2.7k
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Answer: A: EdgeR -ANOVA-like test vs testing individual contrasts
8.4 years ago Aaron Lun ★ 29k
0
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1
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1.8k
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Answer: A: kegga() p-value calculated differently in different edgeR versions
8.4 years ago Aaron Lun ★ 29k
0
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0
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1.5k
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Answer: A: CRISPR/RNAi screen time course analysis
8.4 years ago Aaron Lun ★ 29k
2
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0
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7.2k
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Comment: C: RNAseq with technical replicates: Does it sound right?
8.4 years ago Aaron Lun ★ 29k
0
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0
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1.2k
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Answer: A: Want help in limma analysis
8.4 years ago Aaron Lun ★ 29k
1
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0
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4.6k
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Answer: A: edgeR reinstall failure: edgeR.rdb' is corrupt
8.4 years ago Aaron Lun ★ 29k
2
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0
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3.5k
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Answer: A: Identification of DEGs through limma analysis
8.4 years ago Aaron Lun ★ 29k
3
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1
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4.2k
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Answer: A: Sparse matrices in Bioconductor objects for single-cell analyses
8.4 years ago Aaron Lun ★ 29k
3
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0
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2.1k
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Comment: C: limma: same data in different formats produces different DEG-analysis results
8.4 years ago Aaron Lun ★ 29k
2,880 results • Page 26 of 58
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