Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

<prev • 707 results • page 1 of 71 • next >
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Comment: C: Choosing a threshold for minimum counts in RNAseq
... As I said in my answer, I choose a threshold that lies between the low-logCPM mode and the high-logCPM mode in the logCPM histogram plot. Generally the precise choice of threshold is not important, as long as you choose one in the trough between the two modes. ...
written 9 days ago by Ryan C. Thompson6.1k
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Comment: C: Is there are better way to improve the design via blocking or contrasts while us
... Aaron has already given you a simulated example where FDR calculation after logFC filtering clearly gives the wrong answer, and he has given you a link to a publication with more information about the topic. We have already explained that filtering genes with low average expression is appropriate an ...
written 21 days ago by Ryan C. Thompson6.1k
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Comment: C: Comparing one condition to multiple others using DESeq2 contrasts
... You need to more clearly define what you want to test. Do you want to test for differential expression between S1 and the mean of S2 through S4? Do you want to test whether S1 is significantly different from each of S2 through S4? ...
written 23 days ago by Ryan C. Thompson6.1k
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Answer: A: Will large differences in the number of reads between samples decrease reliabili
... This looks like a reasonable, expected variation in total read counts. All the totals are within one order of magnitude. I don't think the differences in sequencing depth will be a problem for this data. I've used similar methods successfully on data sets with much wider ranges of total counts. ...
written 23 days ago by Ryan C. Thompson6.1k
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Comment: C: Is there are better way to improve the design via blocking or contrasts while us
... This isn't a direct answer, but your FDR calculation is flawed, and will likely result in overstating your significance (i.e. underestimating the true FDR), because you are filtering by logFC, which is not independent of the p-value. You should instead consider using the treat function to test for a ...
written 23 days ago by Ryan C. Thompson6.1k
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Comment: C: Non-used samples changing number of significant genes in limma
... This plot doesn't seem to show the low or mono samples as having any worse quality than the high samples, although the mRNA samples seem to have a higher average quality than almost anything else. And even if they did, I would expect the quality weights to account for that. I'm afraid I don't know e ...
written 4 weeks ago by Ryan C. Thompson6.1k
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Answer: A: Non-used samples changing number of significant genes in limma
... Remember that limma is estimating a single value of the variance for each gene based on all the samples that are provided to it. This same variance value is then used for all tests involving that fitted model. Of course adding more samples also increases the precision of the estimated variance, whic ...
written 4 weeks ago by Ryan C. Thompson6.1k
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Comment: C: Limma: how to account for twin data (both MZ and DZ twins)?
... This is not a direct answer, but have you done anything to quantify the difference in correlation between twins vs the correlation between unrelated individuals? Maybe it will turn out that the excess correlation between twins is not as large as you suspect. I would also try running duplicateCorrela ...
written 4 weeks ago by Ryan C. Thompson6.1k
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Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
... I am using sva in an analysis of my ChIP-Seq data, and I would like to look at a PCA or MDS plot of the data with the effects of surrogate variables subtracted out. Briefly, I use limma's removeBatchEffect to subtract the fitted effects of the surrogate variables and then run plotMDS on the result. ...
sva pca written 5 weeks ago by Ryan C. Thompson6.1k • updated 4 weeks ago by Vegard Nygaard100
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Answer: A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
... My method of choice is to look at the average logCPM distribution of all genes in the data set. Typically you will see a bimodal distribution, with one mode representing expressed genes and the other representing unexpressed genes. You should choose a threshold between the two modes. You can see an ...
written 5 weeks ago by Ryan C. Thompson6.1k

Latest awards to Ryan C. Thompson

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 6 months ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Scholar 6 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 8 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 8 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 8 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Scholar 8 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 19 months ago, created an answer that has been accepted. For A: On the relationship between design and contrasts
Scholar 19 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: DESeq2 how to define my conditions when I want the results comparing a subset of
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Usability of ERCC spike-ins in standard RNAseq experiments
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Accounting for 5'/3' Bias in DESeq 2
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: edger, trended or common dispersion
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Ribosome profiling analysis in DEseq2/limma
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Using multiple tools for differential gene expression analysis as validation
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: edgeR RNA-seq analysis using glm

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