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7
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Answer: A: removeBatchEffect options: design and covariates
updated 6.7 years ago by 50k • written 9.8 years ago by ★ 7.9k
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Answer: A: Prefering Grouping variables or Interaction terms in Experimental Design
6.8 years ago Ryan C. Thompson ★ 7.9k
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885
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Answer: A: LFDR PROPTRUENULL LIMMA
6.8 years ago Ryan C. Thompson ★ 7.9k
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2.2k
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Answer: A: edgeR: How to set model for glmQLFTest in time-course experiment (compared to gl
6.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Exporting normalized counts over final DB windows from csaw
6.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Does LIMMA accept as an input "variance Stabilizing Transformation" generated by
6.8 years ago Ryan C. Thompson ★ 7.9k
2
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Answer: A: Limma validity for only hundreds of genes/metabolites
6.8 years ago Ryan C. Thompson ★ 7.9k
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2.2k
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Answer: A: How to adjust for different cell type mixtures in differential expression analys
6.9 years ago Ryan C. Thompson ★ 7.9k
2
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3.2k
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Answer: A: Filtering DGEList object in edgeR
6.9 years ago Ryan C. Thompson ★ 7.9k
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1.3k
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Answer: A: differentially expressed genes without contrasts
6.9 years ago Ryan C. Thompson ★ 7.9k
2
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1.4k
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Answer: A: pvalue of deseq2
6.9 years ago Ryan C. Thompson ★ 7.9k
3
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1
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5.8k
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Answer: A: RNAseq with technical replicates: Does it sound right?
6.9 years ago Ryan C. Thompson ★ 7.9k
3
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1.4k
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Answer: A: limma: same data in different formats produces different DEG-analysis results
6.9 years ago Ryan C. Thompson ★ 7.9k
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0
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2.0k
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Answer: A: limma for Paired Samples vs. lme
7.0 years ago Ryan C. Thompson ★ 7.9k
3
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2
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1.4k
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Answer: A: interpretation of edgeR multi factor conditions in GLM
7.1 years ago Ryan C. Thompson ★ 7.9k
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1.5k
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Answer: A: DESeq2 high variance in differential expression results
7.1 years ago Ryan C. Thompson ★ 7.9k
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2.3k
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Answer: A: DESeq2 residuals log transformation input for WGCNA
7.1 years ago Ryan C. Thompson ★ 7.9k
5
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2
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4.8k
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Answer: A: Is there any point to TMM-normalize TPM prior to limma-voom?
7.1 years ago Ryan C. Thompson ★ 7.9k
1
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2
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4.9k
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Answer: A: limma blocking and including covariates
7.1 years ago Ryan C. Thompson ★ 7.9k
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0
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862
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Answer: A: DESeq2 input- normalized counts that were processed
7.2 years ago Ryan C. Thompson ★ 7.9k
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1
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2.2k
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Answer: A: DESeq2 model design with unequal number of time points
7.2 years ago Ryan C. Thompson ★ 7.9k
4
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929
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Answer: A: bias correction (an example from ChIP-seq)
7.2 years ago Ryan C. Thompson ★ 7.9k
2
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2.3k
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Answer: A: LIMMA paired analysis adjusting for two continuous variables - microarray data
7.2 years ago Ryan C. Thompson ★ 7.9k
2
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1.2k
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Answer: A: DESeq2 for read count input from 2 different NGS platforms
7.2 years ago Ryan C. Thompson ★ 7.9k
3
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1.2k
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Answer: A: RNASeq testing for differential expression in one condition, equality in another
7.2 years ago Ryan C. Thompson ★ 7.9k
2
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1
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7.1k
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Answer: A: What problem does the MA plot diagnose? And how do you solve it?
7.2 years ago Ryan C. Thompson ★ 7.9k
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1.4k
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Answer: A: DESeq data diagnosis problem (MAplot, dispersion)
7.2 years ago Ryan C. Thompson ★ 7.9k
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1
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1.8k
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Answer: A: DESeq analysis starting from DESeq normalized counts
7.2 years ago Ryan C. Thompson ★ 7.9k
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0
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1.8k
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Answer: A: Can edgeR be used on GO terms?
7.2 years ago Ryan C. Thompson ★ 7.9k
5
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2
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2.0k
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Answer: A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
7.2 years ago Ryan C. Thompson ★ 7.9k
2
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1
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1.2k
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Answer: A: Comparing across sets of regulated genes -- Strategies?
7.3 years ago Ryan C. Thompson ★ 7.9k
1
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1
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1.9k
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Answer: A: limma and edgeR QL strange results
7.3 years ago Ryan C. Thompson ★ 7.9k
1
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1
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10k
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Answer: C: How to interpret plotBCV plots in edgeR
7.3 years ago Ryan C. Thompson ★ 7.9k
2
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1
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6.7k
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Answer: A: DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq
7.3 years ago Ryan C. Thompson ★ 7.9k
1
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1
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2.7k
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Answer: A: the statistical test that DESeq2 use
7.3 years ago Ryan C. Thompson ★ 7.9k
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1
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3.6k
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Answer: A: How to deal with low-depth RNA-Seq within DESeq2 or edgeR
7.3 years ago Ryan C. Thompson ★ 7.9k
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1
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1.3k
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Answer: A: Stuck at "Read counting step", "summarizeOverlaps"
7.3 years ago Ryan C. Thompson ★ 7.9k
4
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1
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1.1k
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Answer: A: What's the relationship between "design" and "contrasts"?
7.4 years ago Ryan C. Thompson ★ 7.9k
1
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1
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2.0k
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Answer: A: Creating design matrix in LIMMA
7.4 years ago Ryan C. Thompson ★ 7.9k
1
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1
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3.3k
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Answer: A: What was the very first paper to describe "limma-trend"?
8.7 years ago • updated 7.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
7.4 years ago Ryan C. Thompson ★ 7.9k
1
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1
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6.6k
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Answer: A: outlier detection of RNAseq samples
7.5 years ago Ryan C. Thompson ★ 7.9k
2
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0
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1.3k
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Answer: A: Removing hidden batch effects in my DESeq2 analysis resulted in lower number of
7.5 years ago Ryan C. Thompson ★ 7.9k
1
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0
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2.7k
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Answer: A: Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray
7.5 years ago Ryan C. Thompson ★ 7.9k
2
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1
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1.4k
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Answer: A: RNA-seq analysis edgeR
7.5 years ago Ryan C. Thompson ★ 7.9k
2
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1
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1.9k
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Answer: A: Limma for paired and unpaired analysis with adjustment for categorical and conti
7.5 years ago Ryan C. Thompson ★ 7.9k
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1
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1.4k
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Answer: A: edgeR time series DMSO correction
7.5 years ago Ryan C. Thompson ★ 7.9k
3
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1
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1.4k
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Answer: A: edgeR RNA-seq analysis using glm
7.5 years ago Ryan C. Thompson ★ 7.9k
1
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1
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1.0k
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Answer: A: 2-Factor Experiment in edgeR, Effect of no reps in one set and two reps in other
7.6 years ago Ryan C. Thompson ★ 7.9k
3
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1
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3.7k
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Answer: A: DE for genes with very low counts using limma.
7.6 years ago Ryan C. Thompson ★ 7.9k
329 results • Page 2 of 7
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