Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

<prev • 777 results • page 2 of 78 • next >
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Answer: A: Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
... You could probably treat the two haplotypes of each gene as if they were alternative splice forms of a single gene, and Salmon should give you a sane answer for the gene counts and effective lengths. ...
written 5 weeks ago by Ryan C. Thompson6.8k
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Comment: C: Filtering step for differential analysis in edgeR
... If all the statistics and QC look good, then the only possible explanations for a non-significant result are a small (or zero) effect size or a large variance (since roughly speaking, significance is determined by effect size / variance). In the case of cancer samples, tissue heterogeneity can contr ...
written 6 weeks ago by Ryan C. Thompson6.8k
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Comment: C: Filtering step for differential analysis in edgeR
... Ok, so you are not using a logFC threshold of 1.2 as you said. You are using a fold change threshold of 1.2, which is roughly a logFC threshold of 0.26. Those are very different. This is why you should provide example code to show what methods and parameter values you have used. In any case, you sh ...
written 6 weeks ago by Ryan C. Thompson6.8k
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Answer: A: Filtering step for differential analysis in edgeR
... A logFC threshold of 1.2 is quite a stringent cutoff. You are ignoring all genes with a fold change less than 2.3 (i.e. 2^1.2). I'm not surprised that relatively few genes pass this threshold. Also note that using separate thresholds for logFC and FDR is suboptimal, since the double filtering may m ...
written 6 weeks ago by Ryan C. Thompson6.8k
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Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Why are negative values a problem? ...
written 6 weeks ago by Ryan C. Thompson6.8k
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Comment: C: Import bamfiles for RNAsequencing analysis
... I'm afraid I can't debug your code line by line. It looks to me like you are trying to cut and paste together pre-existing code from different sources, and that is not going to work. In this case, the summarizeOverlaps line refers to a variable named exonsByGene, but in your previous line of code, y ...
written 6 weeks ago by Ryan C. Thompson6.8k
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Comment: C: Import bamfiles for RNAsequencing analysis
... There is a typo in the code. There is a comma between Hsapiens and UCSC, when there should be a period. Hence, the line of code should be: tx_by_exon <- exonsBy(TxDb.Hsapiens.UCSC.hg38.knownGene) ...
written 6 weeks ago by Ryan C. Thompson6.8k
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Comment: C: Filtering for ATAC-seq
... Peak-calling is separating relevant regions of the genome from irrelevant regions, so it represents a filtering step. The critical point is that your peak calling procedure (like any other filtering procedure) must be blind to the experimental conditions. This ensures that the filter statistic is in ...
written 7 weeks ago by Ryan C. Thompson6.8k
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Answer: A: Question on performing/interpretation results ANOVA-like analysis using limma
... The comments in your code indicate that you believe the p-values for individual contrasts represent post-hoc testing of individual contrasts within the ANOVA test. This is not the case. Since you called decideTests with method="separate", your results are for t-tests of the individual contrasts, con ...
written 7 weeks ago by Ryan C. Thompson6.8k
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Comment: C: Filtering for ATAC-seq
... Merging peaks is definitely not the way to go and will lead to bias. You should read Lun 2014 in which several strategies for summarizing peaks across samples are tested, including merging (i.e. taking the union) and intersecting, and the only strategy that correctly controls Type I error is the one ...
written 7 weeks ago by Ryan C. Thompson6.8k

Latest awards to Ryan C. Thompson

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Scholar 12 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: edger glmQLFit mix glmLRT
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 12 months ago, created an answer that has been accepted. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Popular Question 12 months ago, created a question with more than 1,000 views. For Equivalent of contrasts.fit & multi-contrast decideTests for edgeR?
Scholar 12 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Batch correction in DESeq2
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How does the function model.matrix (to define experimental design) really works
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Scholar 12 months ago, created an answer that has been accepted. For A: Duplicate Correlation with technical replicates
Scholar 12 months ago, created an answer that has been accepted. For A: How does the function model.matrix (to define experimental design) really works
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: ribosome profiling analysis with different dispersions
Popular Question 12 months ago, created a question with more than 1,000 views. For featureCounts segfault
Popular Question 12 months ago, created a question with more than 1,000 views. For Missing as.list generic from AnnotationDbi?
Popular Question 12 months ago, created a question with more than 1,000 views. For Low-count filtering with uneven sequencing depth between samples?
Popular Question 12 months ago, created a question with more than 1,000 views. For Rsubread::featureCounts extremely slow on some annotations
Popular Question 12 months ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 13 months ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?

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