User: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth230
Reputation:
230
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Location:
Australia
Website:
http://www.statsci.org...
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Google Scholar Page
Last seen:
1 week, 2 days ago
Joined:
3 years, 7 months ago
Email:
s****@wehi.edu.au

Posts by Gordon Smyth

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... +1 See also my reply to the same question on Bioconductor: https://support.bioconductor.org/p/107938/#107969 ...
written 9 days ago by Gordon Smyth230
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Comment: C: [edgeR usage] Comparing categories of fewer input variables for differential gen
... Have you actually tried to use glm.nb() to analyze RNA-seq data? That would be much more complicated than edgeR as well being less powerful and increasing the false discovery rate. ...
written 12 months ago by Gordon Smyth230
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Answer: A: edgeR direction of expression and sign of Log Fold Changes
... You code looks correct. Your `up_A` does contain genes up-regulated in condition A vs whatever you set for the reference level of 'condition', and `down_A` does correspond to down-regulated in condition A. ...
written 21 months ago by Gordon Smyth230
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Job: Postdoctoral position, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Australia
... **Research Officer / Senior Research Officer** Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia An opportunity exists for a postdoctoral scientist (Research Officer) to join the Bioinformatics Division of The Walter and Eliza Hall Institute of ...
australia hi-c job written 22 months ago by Gordon Smyth230
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Answer: A: difference between voom and calcNormFactor normalization methods for RNA-Seq ana
... voom is a analysis method, not a normalization method. Your question is a bit like asking: what is the difference between an engine and a steering wheel? The answer is that they are designed to be used together. You can choose between different engines and you could choose between different steering ...
written 22 months ago by Gordon Smyth230
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Answer: A: GSEA For Paired Microarray Data
... The limma package analyses paired experiments for both microarrays and RNA-seq, and has quite a few options for pathway analysis of the results (GO, KEGG, MSigDB etc). ...
written 2.4 years ago by Gordon Smyth230
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Answer: A: Gsea Plot
... You can easily use the limma package to draw a gene set enrichment plot from a set of indices. For example library(limma) barcodeplot(statistic, index=indices) where 'statistic' is the score by which you want to rank the genes and 'indices' is the vector of indices of genes in your set. However ...
written 2.4 years ago by Gordon Smyth230
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Answer: A: dispersion of a gene, what does it mean?
... https://support.bioconductor.org/p/75260/ ...
written 2.4 years ago by Gordon Smyth230
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Answer: A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
... https://support.bioconductor.org/p/74870/ ...
written 2.4 years ago by Gordon Smyth230
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Comment: C: p-values from a distribution of fold-changes
... No it's not possible. Genes with large fold changes but small counts are not necessarily more significant than those with smaller fold changes but larger counts. If you have two treated samples and two untreated, why not use edgeR or DESeq2 in the usual way (which I know you are familiar with from ...
written 2.5 years ago by Gordon Smyth230

Latest awards to Gordon Smyth

Teacher 20 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 2.4 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 3.2 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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