Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth35k
Reputation:
35,360
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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:
2 minutes ago
Joined:
15 years, 10 months ago
Email:
s****@wehi.edu.au

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 • 3,451 results • page 2 of 346 • next >
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Answer: A: voom variance modeling: lowess curve fitting notation misunderstanding?
... Yes, you're quite right that the trend is a function of r rather than of R. See the corrected preprint at: http://www.statsci.org/smyth/pubs/VoomPreprint.pdf I tried to add a correction some years ago to the published article on Genome Biology, but the process was more difficult than I expected, s ...
written 13 days ago by Gordon Smyth35k
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Comment: C: How to get 'previous symbols'? is there HGNC Mart connection?
... alias2Symbol is not outdated and does not make mistakes in conversion. It gives the correct result for all the genes you mention, for example > alias2Symbol("FAM46C") [1] "TENT5C"   ...
written 15 days ago by Gordon Smyth35k
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Comment: C: GZIP ERROR:-2 using featureCounts (Subread)
... Subread version number? You might also interested in: https://www.biorxiv.org/content/early/2018/07/26/377762 ...
written 16 days ago by Gordon Smyth35k
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Answer: A: covert from RGList to uRNAList
... The short answer is that you can't convert an RGList into a uRNAList. You've already confirmed that your raw data doesn't contain all the information needed to make a uRNAList. Going through the intermediary of an RGList can't change that. On the other hand, there are probably plenty of ways to an ...
written 17 days ago by Gordon Smyth35k
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Answer: A: EdgeR: With two treatments, is it equivalent to split into two different models
... The two approaches are not the same because in (1) you estimate two different dispersion parameters for each gene, one for CM and one for NCM, where in (2) you estimate only one dispersion parameter for each gene. Unless there is a massive difference in variability between the CM and NCM sets, we r ...
written 17 days ago by Gordon Smyth35k
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Comment: C: EdgeR RNAseq -- best way to deal with random effects
... Would I be correct to guess that each "mesocosm" in your experiment is a separate physical field station with its own environmental setup? Does any physical station contribute individuals with more than one dose? In other words, do you really have 12 different physical environments or only 3? I woul ...
written 18 days ago by Gordon Smyth35k
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Comment: C: Change default prior.count in glmFit() to match cpm(), aveLogCPM(), etc?
... I agree that having researchers focus too much on the reported fold-changes rather than on the p-values is a frequent problem. We often have to debate this with our own collaborators and migrate them to Treat in some cases. I wouldn't dissuade you from upping the priort.count you use yourself for gl ...
written 24 days ago by Gordon Smyth35k
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Answer: A: masigpro: could not find function "negative.binomial"
... This looks like a bug in the maSigPro package. The maSigPro package imports the MASS package but not in a way that makes the negative.binomial() function available within the p.value() function. So you have to load the MASS package explicitly yourself. Even if you load MASS though, your code doesn' ...
written 25 days ago by Gordon Smyth35k
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Answer: A: Change default prior.count in glmFit() to match cpm(), aveLogCPM(), etc?
... Jenny, thanks for your suggestion, but I don't agree that there a need to increase the default prior.count for glmFit(). The logFC from edgeR are estimated by NB glms. This is an iterative nonlinear procedure that will never agree exactly with linear computations you might do with logCPM values. I ...
written 26 days ago by Gordon Smyth35k
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Comment: C: Remove reads from raw fastq
... No, I can't help because I have no idea what sort of analysis you are trying to do. Why would you run readDNAstringset? I don't know. Regarding thinCounts(), the error message seems pretty self explanatory. thinCounts() operates on a numeric matrix of counts but that's not what readDNAstringset pro ...
written 28 days ago by Gordon Smyth35k

Latest awards to Gordon Smyth

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: How barcode-plot enrichment is calculated?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Scholar 5 weeks ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Removing continuous covariate effects in limma analysis
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: How barcode-plot enrichment is calculated?
Epic Question 5 weeks ago, created a question with more than 10,000 views. For limma moderated t-statistics and B-statistics
Popular Question 5 weeks ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 5 weeks ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Scholar 9 weeks ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Scholar 9 weeks ago, created an answer that has been accepted. For A: Building linear model (age effect on gene expression)
Popular Question 9 weeks 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]
Popular Question 9 weeks 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 9 weeks ago, created a question with more than 1,000 views. For rcmd check does not recognize generic function definitions
Scholar 9 weeks ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Popular Question 9 weeks ago, created a question with more than 1,000 views. For LIMMA - summarization of Illumina probes for same gene
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: conceptual question about FDR, FDR adjusted p-value and q-value
Scholar 3 months ago, created an answer that has been accepted. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: ANOVA-like test via treat() in limma
Scholar 3 months ago, created an answer that has been accepted. For A: How to plot MD plot in limma
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Analysis of pathways using edgeR
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Trouble with Tximport for edgeR
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: nestedF in decideTests: an analogue of Anova with post-hoc t-tests?

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