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Answer: A: Differential expression across gene features
8.4 years ago Ryan C. Thompson ★ 7.9k
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2
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Answer: A: DESeq2::rlog - does it make sense to use it when I don't have duplicates?
8.4 years ago Ryan C. Thompson ★ 7.9k
2
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1.4k
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Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ★ 7.9k
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Comment: C: Unexpected reversal in normalization factors from csaw
8.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Unexpected reversal in normalization factors from csaw
8.5 years ago Ryan C. Thompson ★ 7.9k
2
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3
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1.3k
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Unexpected reversal in normalization factors from csaw
csaw normalization
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ★ 7.9k
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3.5k
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Comment: C: High number of significant DE genes with low baseMean, is this abnormal?
8.5 years ago Ryan C. Thompson ★ 7.9k
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1
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1.5k
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Answer: A: Using edgeR with "traditional" coverage data?
8.5 years ago Ryan C. Thompson ★ 7.9k
1
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1
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3.5k
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Answer: A: High number of significant DE genes with low baseMean, is this abnormal?
8.5 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: Interpreting contrasts in edgeR
8.5 years ago Ryan C. Thompson ★ 7.9k
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4.1k
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Comment: C: Is Limma's removeBatchEffect() and log2() commutative?
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Updated DESeq2 performance on highly replicated yeast RNA-seq data
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Updated DESeq2 performance on highly replicated yeast RNA-seq data
8.5 years ago Ryan C. Thompson ★ 7.9k
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1
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2.2k
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Comment: C: Updated DESeq2 performance on highly replicated yeast RNA-seq data
8.5 years ago Ryan C. Thompson ★ 7.9k
2
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1
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2.7k
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Answer: A: EdgeR - topTags sort up and down?
8.5 years ago Ryan C. Thompson ★ 7.9k
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2.6k
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Comment: C: Accounting for 5'/3' Bias in DESeq 2
8.5 years ago Ryan C. Thompson ★ 7.9k
3
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1
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2.6k
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Answer: A: Accounting for 5'/3' Bias in DESeq 2
8.5 years ago Ryan C. Thompson ★ 7.9k
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6.5k
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Comment: C: "Over-correction" in the size-factors of the DESeq2 package
8.5 years ago Ryan C. Thompson ★ 7.9k
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1
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5.7k
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Comment: C: Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
8.5 years ago Ryan C. Thompson ★ 7.9k
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5.7k
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Answer: A: Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Batch effects in limma
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Batch effects in limma
8.5 years ago Ryan C. Thompson ★ 7.9k
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5.8k
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Comment: C: Importing a BED file with floating point scores?
8.5 years ago Ryan C. Thompson ★ 7.9k
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5.8k
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Comment: C: Importing a BED file with floating point scores?
8.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Importing a BED file with floating point scores?
8.5 years ago Ryan C. Thompson ★ 7.9k
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5.8k
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Answer: A: Importing a BED file with floating point scores?
8.5 years ago Ryan C. Thompson ★ 7.9k
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1
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4.2k
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Comment: C: FourCseq - error countFragmentOverlaps()
8.5 years ago Ryan C. Thompson ★ 7.9k
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1.2k
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Answer: A: RNA-seq genes differentially expressed in combined treatment
8.5 years ago Ryan C. Thompson ★ 7.9k
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6.3k
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Comment: C: Does limma calculate pvalues using log2 fold changes or with linear values?
8.5 years ago Ryan C. Thompson ★ 7.9k
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941
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Comment: C: modeling tissue effect
8.5 years ago Ryan C. Thompson ★ 7.9k
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2.2k
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Answer: A: Filtering before the linear modelling and empirical bayes steps
8.5 years ago Ryan C. Thompson ★ 7.9k
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3.2k
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Comment: C: Conference: BioC 2016: Where Software and Biology Connect, Stanford, 24-26 June
8.5 years ago Ryan C. Thompson ★ 7.9k
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2
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How to evaluate a p-value histogram from treat or other threshold tests?
edger limma deseq2 p-value distribution
updated 8.6 years ago by 51k • written 8.6 years ago by ★ 7.9k
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Comment: C: Adjusted p-value output from Limma different from output using p.adjust?
8.6 years ago Ryan C. Thompson ★ 7.9k
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1
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2.9k
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Answer: C: Adjusted p-value output from Limma different from output using p.adjust?
8.6 years ago Ryan C. Thompson ★ 7.9k
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1
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2.7k
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Comment: C: Estimating dispersions - deseq2 or other
8.6 years ago Ryan C. Thompson ★ 7.9k
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2.7k
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Comment: C: Estimating dispersions - deseq2 or other
8.6 years ago Ryan C. Thompson ★ 7.9k
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2.8k
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Comment: C: Removing unwanted variation (RUV) for paired analysis ?
8.6 years ago Ryan C. Thompson ★ 7.9k
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3.9k
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Comment: C: ANOVA using edgeR
8.6 years ago Ryan C. Thompson ★ 7.9k
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14k
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Comment: C: how DESeq calculates p-value ?
8.6 years ago Ryan C. Thompson ★ 7.9k
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1.2k
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Comment: C: The same statistical test for all multi omic features
8.6 years ago Ryan C. Thompson ★ 7.9k
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14k
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Comment: C: how DESeq calculates p-value ?
8.6 years ago Ryan C. Thompson ★ 7.9k
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14k
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Answer: A: how DESeq calculates p-value ?
8.6 years ago Ryan C. Thompson ★ 7.9k
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1.2k
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Answer: A: EdgeR GLM following voom conversion of counts
8.6 years ago Ryan C. Thompson ★ 7.9k
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1.7k
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Answer: A: Paired analysis and batch effects ?
8.6 years ago Ryan C. Thompson ★ 7.9k
2
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0
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2.7k
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Answer: A: Estimating dispersions - deseq2 or other
8.6 years ago Ryan C. Thompson ★ 7.9k
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0
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6.7k
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Answer: A: HTseq in bioconductor
8.7 years ago Ryan C. Thompson ★ 7.9k
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1.2k
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Comment: C: edger and deseq2 log2FC nornalization
8.7 years ago Ryan C. Thompson ★ 7.9k
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11k
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Comment: C: Deseq2 error estimating size factors -- zeros in count matrix
8.8 years ago Ryan C. Thompson ★ 7.9k
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1
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6.5k
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Comment: C: sva + egdeR - differential expression analysis - RNA-seq data
8.8 years ago Ryan C. Thompson ★ 7.9k
819 results • Page 8 of 17
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