Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth35k
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34,640
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Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Website:
http://www.statsci.org...
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Google Scholar Page
Last seen:
8 hours ago
Joined:
15 years, 7 months ago
Email:
s****@wehi.edu.au

Head of 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.

Posts by Gordon Smyth

<prev • 3,382 results • page 2 of 339 • next >
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Comment: C: edgeR: design matrix for methylation analysis
... The article says: "In the above code, the two library sizes for each sample should be equal. Otherwise, the library size values are arbitrary and any settings would lead to the same P-value." Hence the library sizes must not be recomputed automatically, otherwise they would no longer be equal for ...
written 5 days ago by Gordon Smyth35k
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Comment: C: edgeR: design matrix for methylation analysis
... The statsci.org website was temporarily down. It's up again now. ...
written 5 days ago by Gordon Smyth35k
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Comment: C: GSVA & Limma for DE of Gene Sets using NanoString Data
... Does the gsva_es matrix that you enter to limma have only 3 rows? ...
written 6 days ago by Gordon Smyth35k
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Answer: A: GSVA & Limma for DE of Gene Sets using NanoString Data
... I have no experience with entering GSVA scores into limma, nor with Nanostring in general. I can make a couple of comments though. It's fine to break up the contrasts into groups that are tested separately. In limma, p-value adjustments are usually used to adjust for multiple testing over genes (o ...
written 6 days ago by Gordon Smyth35k
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Answer: A: mroast/fry with gene weights for most or all genes
... Comparing mouse experiment to human For ortholog mapping from mouse to human, my favourite is HUGO HCOP: https://www.genenames.org/cgi-bin/hcop Using estimated logFCs for all genes is bad, because it will be dominated by large logFCs for low count genes, but all the other options should give goo ...
written 6 days ago by Gordon Smyth35k
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Answer: A: Visualization of analysis of multiple cell lines
... First, note that you don't need to manage components of the EList object yourself. Just call plotMDS(EList, ...) and the function will extract the expression scores automatically. To plot subsets of samples, just use standard subsetting operations in R. An EList can be manipulated as if it was a ...
written 9 days ago by Gordon Smyth35k
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Comment: C: Limma: The log2FC of topTable is not equal to Mean(log2CPM) of Basal - Mean(log2
... Note also that the analysis in Law et al (2016), from which OP has taken the logFC, included a batch correction term, another reason why naive subtraction of means will not match the actual computed logFC. With a batch effect, there is no way to compute logFCs other than to fit the weighted linear ...
written 10 days ago by Gordon Smyth35k
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Answer: A: Pre-ranked camera gene set testing with edgeR results
... Hi Jamie, Yes, you can use cameraPR() with the edgeR results. As test statistic, the signed likelihood ratio test statistic would be best: statistic <- sign(logFC) * sqrt(LR) ...
written 11 days ago by Gordon Smyth35k
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Answer: A: Why my limma DEG result in top Table all without significant meaning,showing log
... Not every dataset gives DE results If I understand your question correctly, the situation seems to have that you done an DE analysis between two groups and don't get any significantly DE genes. You don't show the output from summary(decideTests()) but I am guessing that it shows no up or down genes ...
written 13 days ago by Gordon Smyth35k
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Comment: C: Limma example where one comparison gives different results depending on the matr
... That is part of what I mean, but only the tip of the iceberg. An updated limma would need to store genewise QR-decompositions. As well as that, it requires a rewrite of the F-statistic computation, the subsetting of fit objects and other things. There are lots of special cases. Your outlined code d ...
written 15 days ago by Gordon Smyth35k

Latest awards to Gordon Smyth

Appreciated 6 weeks ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Analysis of pathways using edgeR
Scholar 6 weeks ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How do I find up and down regulated genes for each contrast in LIMMA?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: ANOVA-like test via treat() in limma
Scholar 6 weeks ago, created an answer that has been accepted. For A: Building linear model (age effect on gene expression)
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Using write.table with output from topTags [was: report a possible bug of edgeR]
Epic Question 6 weeks ago, created a question with more than 10,000 views. For EdgeR LogCpm and LogFC values calculation
Popular Question 6 weeks ago, created a question with more than 1,000 views. For edgeR - MDS plot
Popular Question 6 weeks ago, created a question with more than 1,000 views. For specifying filenames and celfile.path to ReadAffy()
Scholar 6 weeks ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to plot MD plot in limma
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Scholar 3 months ago, created an answer that has been accepted. For A: How to plot MD plot in limma
Scholar 3 months ago, created an answer that has been accepted. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Scholar 3 months ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Scholar 3 months ago, created an answer that has been accepted. For A: Finding genes respond differently to treatment between many genotype comparison
Scholar 3 months ago, created an answer that has been accepted. For A: Performing differential gene analysis on RT PCR experimental data
Scholar 3 months ago, created an answer that has been accepted. For A: Trouble with Tximport for edgeR
Scholar 3 months ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Scholar 3 months ago, created an answer that has been accepted. For A: Filtering Rna-seq counts
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Trouble with Tximport for edgeR

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