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Answer: A: LFDR PROPTRUENULL LIMMA
7.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: edgeR: How to set model for glmQLFTest in time-course experiment (compared to gl
7.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Exporting normalized counts over final DB windows from csaw
7.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Does LIMMA accept as an input "variance Stabilizing Transformation" generated by
7.4 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: DESeq2: dealing with outliers
7.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Limma validity for only hundreds of genes/metabolites
7.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: How to adjust for different cell type mixtures in differential expression analys
7.4 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Filtering DGEList object in edgeR
7.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: differentially expressed genes without contrasts
7.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: pvalue of deseq2
7.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: pvalue of deseq2
7.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: pvalue of deseq2
7.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: pvalue of deseq2
7.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: RNAseq with technical replicates: Does it sound right?
7.5 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: limma: same data in different formats produces different DEG-analysis results
7.5 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: What is the proper way to modify mcols of a GRanges inside a GRangesList?
7.6 years ago Ryan C. Thompson ★ 7.9k
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What is the proper way to modify mcols of a GRanges inside a GRangesList?
granges metadata
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ★ 7.9k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
7.6 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
7.6 years ago Ryan C. Thompson ★ 7.9k
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12k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
7.6 years ago Ryan C. Thompson ★ 7.9k
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12k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
7.6 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: limma for Paired Samples vs. lme
7.6 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Alternative packages to limma for analysis of microarray datasets
7.6 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
7.6 years ago Ryan C. Thompson ★ 7.9k
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12k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
7.6 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: interpretation of edgeR multi factor conditions in GLM
7.6 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Force DESeq2 to use pseudocounts
7.7 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: DESeq2 high variance in differential expression results
7.7 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: DESeq2 residuals log transformation input for WGCNA
7.7 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Calculating probability of getting xx genes past FDR10%
7.7 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Is there any point to TMM-normalize TPM prior to limma-voom?
7.7 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: limma blocking and including covariates
7.7 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: DESeq2 input- normalized counts that were processed
7.7 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: DESeq2 model design with unequal number of time points
7.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: DESeq2 model design with unequal number of time points
7.8 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: edgeR ANOVA-like analysis
7.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: bias correction (an example from ChIP-seq)
7.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: LIMMA paired analysis adjusting for two continuous variables - microarray data
7.8 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Edge R Issue from a basic differential expression analysis
7.8 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Edge R Issue from a basic differential expression analysis
7.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: DESeq2 for read count input from 2 different NGS platforms
7.8 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
7.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: RNASeq testing for differential expression in one condition, equality in another
7.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: What problem does the MA plot diagnose? And how do you solve it?
7.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: DESeq data diagnosis problem (MAplot, dispersion)
7.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: DESeq analysis starting from DESeq normalized counts
7.8 years ago Ryan C. Thompson ★ 7.9k
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Answer: A: Can edgeR be used on GO terms?
7.8 years ago Ryan C. Thompson ★ 7.9k
5
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Answer: A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
7.8 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: limma and edgeR QL strange results
7.8 years ago Ryan C. Thompson ★ 7.9k
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2.2k
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Comment: C: limma and edgeR QL strange results
7.8 years ago Ryan C. Thompson ★ 7.9k
819 results • Page 4 of 17
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