Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth37k
Reputation:
36,740
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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:
16 years, 2 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 • 3,592 results • page 1 of 360 • next >
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Answer: A: limma: treating multiple variables as random effects in duplicateCorrelation()
... 1. duplicateCorrelation only accepts one variable. You can't specify two random effects. 2. It seems perfectly natural to set tumorType as an ordinary factor. It wouldn't make sense as a random effect. ...
written 12 hours ago by Gordon Smyth37k
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Answer: A: limma random effects and multi level experiments
... The whole purpose of treating a blocking variable as "random" in a linear model is to recover inter-block information about the treatments. For a balanced design like yours, in which every donor receives every treatment, there is no inter-block information to recover because all the blocks receive t ...
written 1 day ago by Gordon Smyth37k
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Answer: A: How to regress phenotype ~ gene + covars in limma?
... You can't do that in limma. limma is designed to regress gene expression on sample characteristics, not the other way around. ...
written 4 days ago by Gordon Smyth37k
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Answer: A: subread gives segfaults when supplied with falsely-identified paired end reads
... I do not get a segmentation error from the Bioconductor package Rsubread (current devel version). Running ``` align(hg38, file1, file2) ``` where `hg38` is the index path and `file1` and `file2` are single-end RNA-seq FastQ files for different samples, the programs simply runs through the files un ...
written 5 days ago by Gordon Smyth37k
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Answer: A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
... You can't use goana() to do a GO analysis of *Olea europaea* because GO annotation doesn't exist for that species. If you type ``` help("goana") ``` then it will tell you to type ``` help("alias2Symbol") ``` for a complete list of species for which goana() will work. You will see that *Olea* is not ...
written 6 days ago by Gordon Smyth37k
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Answer: A: Limma - decideTests - separate/nestedF questions
... https://support.bioconductor.org/p/16689/ ...
written 8 days ago by Gordon Smyth37k
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Comment: C: Help with Limma F.p.value from eBayes
... @SamGG, you haven't compared the F-test to the t-tests correctly. You used an F-test to compare all 5 groups but then conducted only one t-test instead of 4. If you make a fair comparison then the t-tests detect 169 genes and the F-test only 106: ``` > fit <- fit[,-1] > results.t <- dec ...
written 8 days ago by Gordon Smyth37k
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Answer: A: Help with Limma F.p.value from eBayes
... The idea that you propose, using genewise F-tests as a screen before doing t-tests for each coefficient, is easily implemented in limma. In limma terminology, this procedure is called *hierarchical* multiple testing with the F-test as the genewise test. The code would be: ``` fit2 <- fit2[,-1] r ...
written 8 days ago by Gordon Smyth37k
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Comment: C: Voom shows error message:
... I don't know what this has to do with galaxy. You can compute FPKM in R very easily. ...
written 11 days ago by Gordon Smyth37k
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Answer: A: Voom shows error message:
... You can't use limma or voom if you have only two samples without any replication. It is a fundamental truth in statistics that you can't do any statistical analysis given only one observation in each group because there is no way to estimate variability. See for example the commentary here: https:/ ...
written 11 days ago by Gordon Smyth37k

Latest awards to Gordon Smyth

Popular Question 3 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 3 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How barcode-plot enrichment is calculated?
Scholar 3 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Popular Question 4 months ago, created a question with more than 1,000 views. For Genbank to Unigene IDs
Popular Question 4 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 4 months ago, created a post with more than 5 votes. For A: Removing continuous covariate effects in limma analysis
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: How barcode-plot enrichment is calculated?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Removing continuous covariate effects in limma analysis
Appreciated 4 months ago, created a post with more than 5 votes. For A: How barcode-plot enrichment is calculated?
Popular Question 4 months ago, created a question with more than 1,000 views. For specifying filenames and celfile.path to ReadAffy()
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: ANOVA-like test via treat() in limma
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How barcode-plot enrichment is calculated?
Scholar 4 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Appreciated 5 months ago, created a post with more than 5 votes. For A: How barcode-plot enrichment is calculated?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Removing continuous covariate effects in limma analysis
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. 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?
Scholar 5 months ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Popular Question 5 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 5 months ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Epic Question 5 months ago, created a question with more than 10,000 views. For limma moderated t-statistics and B-statistics
Popular Question 6 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 6 months ago, created a question with more than 1,000 views. For rcmd check does not recognize generic function definitions

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