Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth38k
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37,730
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Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Website:
http://www.statsci.org...
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Google Scholar Page
Last seen:
an hour ago
Joined:
16 years, 6 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 • 3,711 results • page 1 of 372 • next >
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Comment: C: Design matrix for cohort with samples outside "block"
... What do the vectors `clusterA`, `clusterB` etc contain? ...
written 2 days ago by Gordon Smyth38k
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Answer: A: What to do when a bug is found in a BioConductor package (Glimma)
... If you type `packageDescription("Glimma")`, or visit the Glimma landing page at the http://bioconductor.org/packages/Glimma, you will see that Glimma has an issues site for reporting bugs or other issues: https://github.com/Shians/Glimma/issues I'm not sure that rounding would be considered a bug ...
written 4 days ago by Gordon Smyth38k
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Comment: C: Limma residuals matrix
... Yes that's right. Using `removeBatchEffect` is not the same as it does not subtract out the intercept. ...
written 4 days ago by Gordon Smyth38k
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Answer: A: Limma residuals matrix
... ``` ResidualsMatrix <- residuals(fit, eset) ``` ...
written 4 days ago by Gordon Smyth38k
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Comment: C: The meaning of interaction terms in design matrix in edgeR User's Guide on page
... Simple arithmetic shows you that the two expressions are exactly the same: (Drug.1h - Placbo.1h) - (Drug.0h - Placebo.0h) = Drug.1h - Placebo.1h - Drug.0h + Placebo.0h = (Drug.1h - Drug.0h) - (Placebo.1h - Placebo.0h) ...
written 5 days ago by Gordon Smyth38k
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Answer: A: The meaning of interaction terms in design matrix in edgeR User's Guide on page
... I appreciate your reading the edgeR User's Guide so carefully. Yes, your understanding is correct but so is the edgeR User's Guide. The `DrugvsPlacebo.1h` and `DrugvsPlacebo.2h` contrasts are defined on page 36 of the Guide, and they are exactly equivalent to what you say they should be. ...
written 5 days ago by Gordon Smyth38k
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Comment: C: Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
... > it should be CvsA=C-A OK. > And it could be better to say: .....genes that are always "significant" in red cells, not always "higher" in last line 6 on page 32, No, the text is correct as it stands. The reference to "higher" is deliberate. ...
written 8 days ago by Gordon Smyth38k
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Answer: A: Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
... Yes, you are right. Thanks for alerting us. Now fixed. ...
written 8 days ago by Gordon Smyth38k
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Comment: C: the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
... I think that you would be well advised to read the documentation that comes with edgeR instead of random posts by anonymous people on stackexchange. The edgeR User's Guide has a section on pseudo counts that says: > The pseudo-counts are computed for a specific purpose, and their computation dep ...
written 8 days ago by Gordon Smyth38k
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Answer: A: How to create two columns for model matrix used in limma?
... The 3rd coefficient *is* the contrast of D2 vs D1. Just test the 3rd coefficient. In your case, you don't actually need to use `makeContrasts` at all. You could just use ``` design <- model.matrix(~ gender + drug) ``` and then later test for ``` topTable(fit, coef=2) topTable(fit, coef=3) ``` to ...
written 9 days ago by Gordon Smyth38k

Latest awards to Gordon Smyth

Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Scholar 9 days ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 14 days ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 26 days ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 29 days ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 4 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Scholar 4 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 4 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Popular Question 7 months ago, created a question with more than 1,000 views. For non-integer counts for edgeR
Scholar 7 months ago, created an answer that has been accepted. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Popular Question 7 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Popular Question 7 months ago, created a question with more than 1,000 views. For Columns used by read.maimages for Agilent arrays
Scholar 7 months ago, created an answer that has been accepted. For A: barcodeplot how to increase the font size
Popular Question 7 months ago, created a question with more than 1,000 views. For File format for single channel analysis of Agilent microarray data with Limma?
Popular Question 7 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Popular Question 7 months ago, created a question with more than 1,000 views. For simultaneous use of robust and weighting methods in limma
Scholar 7 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Popular Question 7 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]
Popular Question 7 months ago, created a question with more than 1,000 views. For Estimating fold change from limma 'log2FC' using lumi
Popular Question 7 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?
Scholar 7 months ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Appreciated 7 months ago, created a post with more than 5 votes. For A: Removing continuous covariate effects in limma analysis
Appreciated 7 months ago, created a post with more than 5 votes. For A: Volcanoplot with limma - RAW P-values or Adj.P-Values

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