User: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth280
Reputation:
280
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Location:
Australia
Website:
http://www.statsci.org...
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1 week ago
Joined:
4 years, 4 months ago
Email:
s****@wehi.edu.au

Posts by Gordon Smyth

<prev • 24 results • page 1 of 3 • next >
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Answer: A: How to see if adjusting batch effect in RNA-seq is working or not
... It seems that everything is actually working correctly, except that you are not making the PCA plot correctly. As you already know, to make an MDS plot in edgeR, you can type plotMDS(logCPM_TMM) To make an PCA plot, you just use plotMDS(logCPM_TMM, gene.selection="common") When you set ...
written 8 days ago by Gordon Smyth280
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Comment: C: How many tests does it take to warrant a microarray/RNA-seq approach to differen
... Using edgeR, DESeq or DESeq (or any NB-based software) for PCR data is not at all appropriate, and for reasons that run much deeper than whether the values are integer or not. Use limma or HTqPCR (a limma wrapper) instead (and ordinary limma, not voom). ...
written 3 months ago by Gordon Smyth280
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Answer: A: Why my limma DEG result in top Table all without significant meaning,showing log
... The Agi4x44PreProcess package was removed from Bioconductor many years ago. You must be using very old versions of R and Bioconductor. I would certainly not advise you to preprocess the Agilent microarray data in the complicated way that you have. Why not use more up-to-date software and a pipeline ...
written 4 months ago by Gordon Smyth280
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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 months ago by Gordon Smyth280
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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 21 months ago by Gordon Smyth280
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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 2.5 years ago by Gordon Smyth280
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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 2.6 years ago by Gordon Smyth280
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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 2.6 years ago by Gordon Smyth280
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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 3.1 years ago by Gordon Smyth280
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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 3.1 years ago by Gordon Smyth280

Latest awards to Gordon Smyth

Teacher 8 days ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 3.2 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 4.0 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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