Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

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Comment: C: skewed differentially expressed gene results - DESeq2
... There is no point in filtering for low within-group variance. DESeq2 is already doing this when it assesses the the significance of each gene and computes a p-value and adjusted p-value. If these outlier samples are to blame for what you believe to be false positive genes, then the problem is not wi ...
written 14 days ago by Ryan C. Thompson ♦ 6.8k
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Answer: A: skewed differentially expressed gene results - DESeq2
... Is it possible that the same 3 or 4 samples are outliers in many genes? If so, it might help if you redo your analysis with limma using voomWithQualityWeights. This will hopefully identify and down-weight the samples that are consistently outliers across many genes. You can also inspect the weights ...
written 14 days ago by Ryan C. Thompson ♦ 6.8k
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Comment: C: skewed differentially expressed gene results - DESeq2
... I don't think these results are obviously being skewed by the 3 highest samples in the "yes" group. Even if you ignore these, the "yes" group still has a higher average normalized count than the "no" group. It might not be as significant without the 3 highest samples, but I wouldn't say that this ge ...
written 14 days ago by Ryan C. Thompson ♦ 6.8k
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Comment: C: unexpected p-value histogram in edgeR
... Sorry, I think I explained poorly. I didn't mean that different contrasts could have different BCV values. I meant that if one contrast involves only samples in the data set with lower-than-average variability, then the null distribution of logFC values will be smaller than expected for the whole-da ...
written 7 weeks ago by Ryan C. Thompson ♦ 6.8k
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Comment: C: unexpected p-value histogram in edgeR
... I have seen the type of p-value distribution that you are seeing in similar situations. Specifically, when a particular contrast has both little to no real differential expression and low biological variability relative to other contrasts in the same data set. The result is that the null distributio ...
written 7 weeks ago by Ryan C. Thompson ♦ 6.8k
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Answer: A: DESseq2: Why can the dispersion be generelized over the conditions?
... The core issue is that if you want to estimate more parameters (such as additional dispersions for each group), you need more data. DESeq2 shares dispersion information between genes to make up for the fact that the data for a single gene is already insufficient to yield a stable estimate of even a ...
written 7 weeks ago by Ryan C. Thompson ♦ 6.8k
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Comment: C: DESeq Timepoint Design (using Baseline as reference)
... Are you trying to identify specific genes that have different response in the two conditions, or are you just trying to determine whether the two gene signatures are distinct? ...
written 11 weeks ago by Ryan C. Thompson ♦ 6.8k
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Comment: C: How to get the ordinary t statistic for two paired groups?
... Oh, sorry, I didn't notice that detail. Please disregard my answer. ...
written 11 weeks ago by Ryan C. Thompson ♦ 6.8k
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Answer: A: How to get the ordinary t statistic for two paired groups?
... I believe the default for t.test is to assume unequal group variances, while limma assumes equal variances. I'm not sure how much of a discrepancy you are seeing, but this might explain the difference. ...
written 11 weeks ago by Ryan C. Thompson ♦ 6.8k
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Comment: C: How to obtain a normalised expression matrix from read counts and scaling factor
... It would be easiest if you used the DGEList class to contain both the counts and normalization factors. For example: dge <- DGEList(matrix) dge_tmm <- calcNormFactors(dge, method="TMM") cpm(dge_tmm) ...
written 11 weeks ago by Ryan C. Thompson ♦ 6.8k

Latest awards to Ryan C. Thompson

Teacher 11 weeks 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
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For summarizeOverlaps using GRanges or bed file as reads?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Popular Question 11 weeks ago, created a question with more than 1,000 views. For edgeR Quasi-likelihood with tagwise dispersion?
Scholar 3 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 14 months ago, created an answer that has been accepted. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 14 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 14 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 14 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 14 months ago, created an answer that has been accepted. For A: Duplicate Correlation with technical replicates
Scholar 14 months ago, created an answer that has been accepted. For A: How does the function model.matrix (to define experimental design) really works
Appreciated 14 months ago, created a post with more than 5 votes. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Student 14 months ago, asked a question with at least 3 up-votes. For Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Batch correction in DESeq2
Popular Question 14 months ago, created a question with more than 1,000 views. For Low-count filtering with uneven sequencing depth between samples?
Popular Question 14 months ago, created a question with more than 1,000 views. For Missing as.list generic from AnnotationDbi?
Popular Question 14 months ago, created a question with more than 1,000 views. For Rsubread::featureCounts extremely slow on some annotations
Popular Question 14 months ago, created a question with more than 1,000 views. For Equivalent of contrasts.fit & multi-contrast decideTests for edgeR?
Scholar 14 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: edger glmQLFit mix glmLRT
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: ribosome profiling analysis with different dispersions
Popular Question 14 months ago, created a question with more than 1,000 views. For featureCounts segfault
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