User: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth1.4k
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Australia
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http://www.statsci.org...
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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 • 97 results • page 1 of 10 • next >
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Comment: C: RNA-seq differential analysis with N batches and a technical replicate in each b
... The Bioconductor thread doesn't seem similar to me. ...
written 8 days ago by Gordon Smyth1.4k
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Answer: A: RNA-seq differential analysis with N batches and a technical replicate in each b
... You have included a technical replicate in each batch, but a technical replicate of what? A replicate of the same sample in every batch? Anyway, including batch as a blocking factor seems the obvious and best approach. You can easily assess variance between batches by testing for differential expre ...
written 8 days ago by Gordon Smyth1.4k
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Answer: A: The error generated by Rsamtools
... Rsubread can sort and index the BAM file on-the-fly during the alignment. It is much faster to take advantage of that facility than to sort and index the BAM file afterwards. `indexBAM` might perhaps assume that the BAM file is location-sorted but, by default, it won't be. ...
written 8 days ago by Gordon Smyth1.4k
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Comment: C: What Does Requirebothendsmapped From Rsubread Package Means?
... The former, not the latter. The paired reads do not both have to overlap the same feature or meta-feature. In other words, the option does exactly what the documentation says and does not do anything extra that is not stated. ...
written 18 days ago by Gordon Smyth1.4k
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Answer: A: RNA Seq data with GSEA
... I am the voom author, but I do not recommend voom for this purpose because GSEA is unable to use the voom precision weights. Just use: ``` y <- DGEList(counts ...) y <- calcNormFactors(y) GSEA_table <- cpm(y, log=TRUE) ``` You do not need `filterByExpr` here but, if you do use it, it shou ...
written 24 days ago by Gordon Smyth1.4k
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Answer: A: featurecounts output changes the underscores in the sample name into dots
... No, you can't avoid the conversion. featureCounts is trying to protect the names from systems that can't handle punctuation in variable names, but I agree it is not necessary here. Of course you had to input the file names to `featureCounts` in the first place: ``` fc <- featureCounts(files, .. ...
written 24 days ago by Gordon Smyth1.4k
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Comment: C: limma voom problem
... I had a closer look at your design matrix and realized that there are other issues with your use of `voom` of even more immediate concern that the number of columns in the design matrix. I have edited my answer above to explain. ...
written 28 days ago by Gordon Smyth1.4k
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Comment: C: limma voom problem
... It is a universal statistical principle, not specific to limma, that you can't estimate more parameters than you have data points. If you fit a linear regression with as many coefficients as data points, then all the residuals will be zero regardless of the unknown variance of the data. How could yo ...
written 28 days ago by Gordon Smyth1.4k
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Answer: A: Design matrix for voom: with or without batch blocking?
... See Chapter 15 (RNA-seq Data) in the limma User's Guide. The comments there apply to proteomics counts as well as RNA-seq. Heteroscedasticity is examined in limma by either a `voom` plot (for the voom pipeline) or `plotSA` (for the limma-trend pipeline. Standard univariate heterscedasticity analyse ...
written 29 days ago by Gordon Smyth1.4k
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Answer: A: limma voom problem
... Actually, it is not possible to get the message you show if you entered a valid count matrix to `voom` with the design matrix that you show. There are only two possibilities. Either 1. Your count matrix contains NA values (which are not allowed, see the voom help page) or 2. The design matrix enter ...
written 29 days ago by Gordon Smyth1.4k

Latest awards to Gordon Smyth

Scholar 8 weeks ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 12 weeks ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Guru 4 months ago, received more than 100 upvotes.
Teacher 4 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 7 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 10 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 11 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 11 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 11 months ago, created an answer that has been accepted. For A: Differential expression: replicates in one condition, no replicates in the other
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Good Answer 11 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 11 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 11 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 11 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis

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