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Comment: C: limma - technical replicates: duplicateCorrelation() or avereps()?
8.3 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: DE for genes with very low counts using limma.
8.3 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: DE for genes with very low counts using limma.
8.3 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Usability of ERCC spike-ins in standard RNAseq experiments
8.3 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
8.3 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Unusual skewed MA plot at lower expression
8.3 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Unusual skewed MA plot at lower expression
8.3 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
8.3 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: DEseq normalization Small RNA-seq data using rRNA
8.3 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: DEseq2 normalization Small RNA-seq data using rRNA
8.3 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: voom + removeBatchEffect + gene clustering
8.3 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: limma-voom or edgeR for paired designs both within and between comparisons
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Coping with a label/class imbalance in DESeq2
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Coping with a label/class imbalance in DESeq2
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Coping with a label/class imbalance in DESeq2
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Coping with a label/class imbalance in DESeq2
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Coping with a label/class imbalance in DESeq2
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Coping with a label/class imbalance in DESeq2
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Coping with a label/class imbalance in DESeq2
8.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Coping with a label/class imbalance in DESeq2
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Help with Two-way ANOVA in Limma
8.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Help with Two-way ANOVA in Limma
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: [Limma] Testing continuous variable with interaction
8.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: [Limma] Testing continuous variable with interaction
8.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: edgeR: Nested interactions model matrix MISSING COEFFICIENTS
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
8.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: On the relationship between design and contrasts
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Duplicate Correlation with technical replicates
8.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Duplicate Correlation with technical replicates
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Bootstrap confidence intervals on RNA-seq expression from Kallisto
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell d
8.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Appropriate ways to filter counts data for voom/limma
8.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: makeTxDbFromBiomart fails on Ensembl 85 human
8.5 years ago Ryan C. Thompson ★ 7.9k
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makeTxDbFromBiomart fails on Ensembl 85 human
biomart maketxdbfrombiomart genomicfeatures
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: makeTxDbFromBiomart fails on Ensembl 85 human
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: regularized log transformation- loss of zero values for sparsely expressed genes
8.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: About differentially expressed genes that found by edgeR
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Please share me your helpful comments with edgeR analysis without replicate
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Please share me your helpful comments with edgeR analysis without replicate
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Low percentage of assigned fragments with FeatureCounts
8.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Please help with estimating dispersion value using housekeeping genes in edgeR
8.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: How to analyze single channel extremely raw data with LIMMA
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: limma lmFit coefficients and p-values
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: limma lmFit coefficients and p-values
8.5 years ago Ryan C. Thompson ★ 7.9k
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11k
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Comment: C: limma lmFit coefficients and p-values
8.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: 3 replicates vs 2 replicates biased outcome?
8.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Fit a multinomial to RNA-seq count data
8.6 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: What is the correct contrast matrix if one treatment must be compared to both of
8.6 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: What's the rationale for using the negative binomial distribution to model read
8.6 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: limma roast/mroast with patient-matched pre-/post- treatment
8.6 years ago Ryan C. Thompson ★ 7.9k
819 results • Page 6 of 17
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