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Comment: C: limma random effects and multi level experiments
5.5 years ago mikhael.manurung ▴ 280
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0
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1.4k
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Comment: C: How to regress phenotype ~ gene + covars in limma?
5.5 years ago mikhael.manurung ▴ 280
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1.3k
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Comment: C: LIMMA how to model unidentified source of covariate
5.5 years ago mikhael.manurung ▴ 280
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1
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2.0k
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Comment: C: Flow cytometry optimization of transformation parameters
5.6 years ago mikhael.manurung ▴ 280
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0
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3.0k
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Comment: C: Useful of Normal Enrichment Score (NES) in GSEA
5.6 years ago mikhael.manurung ▴ 280
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1
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1.9k
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Comment: C: Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
5.6 years ago mikhael.manurung ▴ 280
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0
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1.1k
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Comment: C: Cydar's countCells tolerance parameter for arcsinh-transformed data
5.6 years ago mikhael.manurung ▴ 280
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1
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1.1k
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Comment: C: Cydar's countCells tolerance parameter for arcsinh-transformed data
5.6 years ago mikhael.manurung ▴ 280
1
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0
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28k
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Comment: C: DESeq2 log2FC shrink before GSEA or not?
5.6 years ago mikhael.manurung ▴ 280
2
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4
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1.1k
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Cydar's countCells tolerance parameter for arcsinh-transformed data
cydar CyTOF
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 280
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1
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1.5k
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Comment: C: variancePartition - testing for individuals
5.6 years ago mikhael.manurung ▴ 280
0
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1
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1.5k
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Comment: C: variancePartition - testing for individuals
5.6 years ago mikhael.manurung ▴ 280
0
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0
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815
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Comment: C: Comparing groups with paired samples by using limma
5.6 years ago mikhael.manurung ▴ 280
0
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1
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1.5k
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Answer: A: variancePartition - testing for individuals
5.7 years ago mikhael.manurung ▴ 280
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0
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1.5k
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Comment: C: Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
5.7 years ago mikhael.manurung ▴ 280
0
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1
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906
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Comment: C: Limma time course experiments
5.7 years ago mikhael.manurung ▴ 280
0
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0
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2.4k
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Comment: C: Controlling numerical covariates: differential gene expression with limma voom
5.8 years ago mikhael.manurung ▴ 280
0
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1
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2.6k
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Comment: C: Count filter for differential expression
5.8 years ago mikhael.manurung ▴ 280
0
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0
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945
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Comment: C: RNA seq analysis
5.8 years ago mikhael.manurung ▴ 280
3
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1
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2.4k
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Answer: A: Controlling numerical covariates: differential gene expression with limma voom
5.8 years ago mikhael.manurung ▴ 280
0
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0
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1.7k
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Comment: C: nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
6.0 years ago mikhael.manurung ▴ 280
0
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0
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1.7k
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Comment: C: nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
6.0 years ago mikhael.manurung ▴ 280
0
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2
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1.7k
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Comment: C: nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
6.0 years ago mikhael.manurung ▴ 280
0
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1
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2.4k
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Comment: C: extracting the genes associated with the groups or samples in pheatmap.
6.0 years ago mikhael.manurung ▴ 280
5
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6
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1.7k
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nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
limma anova decidetests
updated 6.0 years ago by 51k • written 6.0 years ago by ▴ 280
0
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0
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1.6k
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Comment: C: Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
6.0 years ago mikhael.manurung ▴ 280
0
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1
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1.6k
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Comment: C: Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
6.0 years ago mikhael.manurung ▴ 280
5
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5
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1.6k
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Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 6.0 years ago by 67k • written 6.0 years ago by ▴ 280
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0
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2.4k
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Comment: C: Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
6.0 years ago mikhael.manurung ▴ 280
0
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0
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2.4k
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Comment: C: Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
6.0 years ago mikhael.manurung ▴ 280
6
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5
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2.4k
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Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq mixed model repeated measures
updated 6.0 years ago by 51k • written 6.0 years ago by ▴ 280
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