Moderator: Gordon Smyth

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Gordon Smyth30k
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Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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Head of Bioinformatics Division at the Walter and Eliza Hall Institute of Medical Research

Posts by Gordon Smyth

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Answer: A: illumina ht-12 v4 expression beadchip
... limma processes this sort of data easily. The key is to use the arguments of read.ilmn() to tell limma how the columns are named in the data file from GEO. Here is a quick limma analysis of GSE74629: > library(limma) > x <- read.ilmn("GSE74629_non-normalized.txt",expr="SAMPLE ",probeid="I ...
written 1 day ago by Gordon Smyth30k
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Comment: C: illumina ht-12 v4 expression beadchip
... Yes, limma will read and process those columns. See my answer below. ...
written 1 day ago by Gordon Smyth30k
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Answer: A: edgeR bcvvalue related significant number of genes
... The best you can do is to choose a sensible BCV value based on your experience with similar plant samples where you did have replicates. In the absence of replicates, the aim is more to rank to genes rather than to obtain a rigorous measure of statistical significance. Sorry, there's no "right" val ...
written 2 days ago by Gordon Smyth30k
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Answer: A: apply edgeR TMM normalization without converting data format into 'DGEList'
... After downstream analysis, can I say that I have applied TMM method for normalisation? Well, it depends on what downstream analysis you do, which you haven't told us anything about. How can we comment on things you don't tell us? ...
written 3 days ago by Gordon Smyth30k
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Comment: C: correction for batch effects and paired-design of RNA-seq samples
... You can use removeBatchEffect() for the MDS plot. That's the main purpose of the function, for plotting purposes. ...
written 3 days ago by Gordon Smyth30k
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Answer: A: correction for batch effects and paired-design of RNA-seq samples
... There is no need to do any batch correction. The baseline differences between subjects, including any batch effect, is already accounted for in the paired analysis. ...
written 3 days ago by Gordon Smyth30k
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Comment: C: General suggestions regarding gene expression
... If you were my student, I would want to be consulted rather than surprised. And I would probably advise you to collaborate with a bioinformatician and to concentrate your own time on the immunological science rather than trying to be a part-time bioinformatician yourself. If you are simply trying t ...
written 4 days ago by Gordon Smyth30k
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Comment: C: running off target analaysis
... I see this is your first post. Welcome to Bioconductor! A few tips. Please post your question as a "Question" rather than as a "Tutorial" -- you're not offering a tutorial! Please tag your question with the name of package you want help with -- I've done that for you now. Please don't post answers ...
written 4 days ago by Gordon Smyth30k
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Answer: A: Camera gene set interpretation
... You could use camera(final.table, indices, des, contrast=c(-1,1)) But why not make it even easier: des <- model.matrix(~group) camera(final.table, indices, des) ...
written 4 days ago by Gordon Smyth30k
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Comment: C: How to interpret plotBCV plots in edgeR
... Well, the RNA-seq libraries seem somewhat like single cell libraries, although not as extreme. Perhaps the samples are just very variable. Note that normalization is always an issue for single cell RNA-seq, and may be for your data as well. Default use of calcNormFactors() in edgeR might not be app ...
written 5 days ago by Gordon Smyth30k

Latest awards to Gordon Smyth

Scholar 3 days ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Great Question 12 days ago, created a question with more than 5,000 views. For EdgeR LogCpm and LogFC values calculation
Scholar 14 days ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 15 days ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 16 days ago, created a question with more than 1,000 views. For LIMMA - summarization of Illumina probes for same gene
Popular Question 18 days ago, created a question with more than 1,000 views. For LIMMA - summarization of Illumina probes for same gene
Scholar 27 days ago, created an answer that has been accepted. For A: Question about genas function in the limma package
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: limma-voom when testing differential expression of a subset of genes.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Error when fitting linear model with technical replicates and blocking variable
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: limma-voom for miRNA seq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Calculating a p value by permutation analysis
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Confidence intervals on edgeR logFC
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Fit a multinomial to RNA-seq count data
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: In limma's barcode plot, why are the cutoffs for the pale red and blue bands +/-
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Effect size similar to Cohen's d in limma
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Effects of continuous variable with adjustment for gender
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Possible ways of performing differential gene expression and analysis of RNA-Seq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR

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