User: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth840
Reputation:
840
Status:
Trusted
Location:
Australia
Website:
http://www.statsci.org...
Scholar ID:
Google Scholar Page
Last seen:
15 hours ago
Joined:
4 years, 10 months ago
Email:
s****@wehi.edu.au

Joint Head of the 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, all part of the Bioconductor project.

Posts by Gordon Smyth

<prev • 56 results • page 1 of 6 • next >
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Answer: A: limma voom - mean variance trend
... No, I've never seen a voom plot like that (concave decreasing) and there are no situations I can think of in which it should arise. The standard deviations look very large indeed, so there may be systematic lack of fit (a missing covariate). If I were you I'd go back and look at the raw counts to ch ...
written 19 days ago by Gordon Smyth840
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Answer: A: diffSplice: Error in exon.genes[o, , drop = FALSE] : incorrect number of dimensi
... `diffSplice` has been used many times and is pretty robust. I am unable to reproduce the error you report even by deliberating giving incorrect input to the function. I have to assume that there is something wrong with your input data or, possibly, that you have an ancient version of the software. ...
written 19 days ago by Gordon Smyth840
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Answer: A: edgeR : How to test differential exon usage on case/control study across all tim
... https://support.bioconductor.org/p/98699/ ...
written 19 days ago by Gordon Smyth840
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... The error is telling you that your annotation matrix doesn't match with the expression matrix. You have to make sure that the rows of your annotation matrix corresponds to the columns of the expression matrix, which at present they don't. How can you expect to correlate GA with expression if you don ...
written 23 days ago by Gordon Smyth840
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... Using `0+` in the model.matrix formula is unnecessary and incorrect. Why are you forcing the regression to go through zero? Just remove it and the remaining limma code will run fine. ...
written 28 days ago by Gordon Smyth840
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Comment: C: How to filter out probsets and genes from Affymetrix microarray expression data
... IMO it is best not to remove the cross-posts at this stage because they've already been answered. Removing the duplicate questions would also remove people's answers. ...
written 4 weeks ago by Gordon Smyth840
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Comment: C: How to filter out probsets and genes from Affymetrix microarray expression data
... Very similar questions cross posted to Bioconductor: - https://support.bioconductor.org/p/121936 - https://support.bioconductor.org/p/122063 ...
written 4 weeks ago by Gordon Smyth840
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Answer: A: Could not reproduce the results (MA-plot) in the paper when analyzing two-color
... It can be hard to reproduce published analyses exactly, unless the authors provide exact code, but I can see several discrepancies between the authors' stated protocol and your code. The most important discrepancy is that you haven't filtered any spots. The authors removed spots with low intensitie ...
written 10 weeks ago by Gordon Smyth840
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Answer: A: EdgeR: Filtering Counts Relationship to Sigficance.
... https://support.bioconductor.org/p/120593/ ...
written 11 weeks ago by Gordon Smyth840
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Comment: C: EdgeR: Filtering Counts Relationship to Sigficance.
... The edgeR authors answer questions promptly on Bioconductor and prefer that the same question not to be cross-posted to other forums at the same time, because it takes more of our time to monitor and because questions may get left hanging. I answered your question on Bioconductor about an hour after ...
written 11 weeks ago by Gordon Smyth840

Latest awards to Gordon Smyth

Scholar 19 days ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 4 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Scholar 4 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Scholar 4 months ago, created an answer that has been accepted. For A: Differential expression: replicates in one condition, no replicates in the other
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Differential expression: replicates in one condition, no replicates in the other
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: edgeR - DE with one disease sample vs. multiple control samples?
Scholar 4 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 5 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 3.7 years ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis

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