Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth37k
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37,270
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Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Website:
http://www.statsci.org...
Scholar ID:
Google Scholar Page
Last seen:
42 minutes ago
Joined:
16 years, 4 months ago
Email:
s****@wehi.edu.au

Joint Head of Bioinformatics Division at the Walter and Eliza Hall Institute of Medical Research.

My research group created the limma, edgeR, goseq, Rsubread, csaw and diffHic packages.

Posts by Gordon Smyth

<prev • 3,668 results • page 1 of 367 • next >
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Comment: C: Combining multiple L2FC values and determining variance
... > Getting the average L2FC is easy As I said above, you need an average log-expression value for every sample, not an average logFC. You can't compute variability from an average log-fold-change, which is just one value across all samples. > I just don't know how to properly estimate the err ...
written 11 hours ago by Gordon Smyth37k
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Comment: C: Majority upregulated genes in edgeR
... What makes you say that there are more genes up-regulated in the disease state than down-regulated? You don't show any results that would suggest that. It's certainly not true that edgeR tends to give positive logFCs regardless of what is tested. The signs of the logFCs will in fact just reverse if ...
written 11 hours ago by Gordon Smyth37k
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Answer: A: Normalized count in edger
... Neither of your suggestions are correct -- the quantities you suggest don't really have any meaning. Please see the section on normalization in the edgeR User's Guide. The normalization factors in edgeR serve to normalize the library sizes rather than the counts themselves. In fact, as I have said ...
written 13 hours ago by Gordon Smyth37k
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Answer: A: Combining multiple L2FC values and determining variance
... What you are trying to do is called a *gene set test*, and you should use a gene set test method that allows for the possibility of correlations between the genes. Trying to pool errors as if the genes were independent can markedly underestimate the true variability if the genes are positively corre ...
written 1 day ago by Gordon Smyth37k
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Comment: C: MDS plotting within the limma/voom workflow
... Yes, the `cpm` and the `vst` functions are both transforming the counts to a log scale suitable for a PCA or MDS plot. They have the same aim. In both cases, these transformations are independent of the DE analysis. The output of cpm/vst is not used for the DE analysis, nor is the output of the DE ...
written 1 day ago by Gordon Smyth37k
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Answer: A: MDS plotting within the limma/voom workflow
... In the *RNA-seq analysis is easy as 1-2-3* workflow, `plotMDS` is applied to logCPM values that have been computed using edgeR's `cpm` function with a large prior count. Here the mean-variance relationship inherent in the original counts has been stabilized first by logging and secondly by the large ...
written 2 days ago by Gordon Smyth37k
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Comment: C: limma: How to define correct design matrix for fitting linear model and keep hig
... Cross-posted: https://www.biostars.org/p/385777/#386066 ...
written 3 days ago by Gordon Smyth37k
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Comment: C: bug in "dispersion" argument in edgeR - rpkmByGroup
... The combination of R and limma versions you have will not run correcly, as has been noted here: https://stat.ethz.ch/pipermail/bioc-devel/2019-June/015240.html You could either install R 3.6.0, or else down-grade limma and edgeR to Bioconductor 3.8 versions designed for R 3.5.X. In either case, eve ...
written 5 days ago by Gordon Smyth37k
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Answer: A: bug in "dispersion" argument in edgeR - rpkmByGroup
... Yes, that is a bug, which was introduced to edgeR in the last Bioconductor release. I have fixed it now in edgeR 3.26.5. Thanks for the heads-up. It is curious that you are running versions of limma and edgeR from the Bioconductor 3.9 release under R 3.5.1. Bioconductor 3.9 is designed for R 3.6.0, ...
written 6 days ago by Gordon Smyth37k
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Comment: C: Any efficient workaround to identify highly variable genes in Affymetrix microar
... Yes, that is the correct way to compute the unlog-scale CV from the log-scale SD, but do you appreciate that filtering on SD is exactly the same as filtering on CV, so there is actually no need to compute CV? ...
written 6 days ago by Gordon Smyth37k

Latest awards to Gordon Smyth

Popular Question 5 months ago, created a question with more than 1,000 views. For Using write.table with output from topTags [was: report a possible bug of edgeR]
Scholar 5 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How barcode-plot enrichment is calculated?
Scholar 5 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Popular Question 6 months ago, created a question with more than 1,000 views. For Genbank to Unigene IDs
Popular Question 6 months ago, created a question with more than 1,000 views. For Using write.table with output from topTags [was: report a possible bug of edgeR]
Appreciated 6 months ago, created a post with more than 5 votes. For A: Removing continuous covariate effects in limma analysis
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How barcode-plot enrichment is calculated?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Removing continuous covariate effects in limma analysis
Appreciated 6 months ago, created a post with more than 5 votes. For A: How barcode-plot enrichment is calculated?
Popular Question 6 months ago, created a question with more than 1,000 views. For specifying filenames and celfile.path to ReadAffy()
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: ANOVA-like test via treat() in limma
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How barcode-plot enrichment is calculated?
Scholar 6 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Appreciated 7 months ago, created a post with more than 5 votes. For A: How barcode-plot enrichment is calculated?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Removing continuous covariate effects in limma analysis
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: How barcode-plot enrichment is calculated?
Scholar 7 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Scholar 7 months ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Popular Question 7 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 7 months ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Epic Question 7 months ago, created a question with more than 10,000 views. For limma moderated t-statistics and B-statistics
Popular Question 8 months ago, created a question with more than 1,000 views. For How do I find up and down regulated genes for each contrast in LIMMA?
Popular Question 8 months ago, created a question with more than 1,000 views. For rcmd check does not recognize generic function definitions

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