Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth35k
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34,940
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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:
51 minutes ago
Joined:
15 years, 8 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 • 3,409 results • page 1 of 341 • next >
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Answer: A: Any difference between v$E and cpm(keep,log=TRUE)
... I have always recommended and used cpm() with log=TRUE and prior.count between 2 and 5, for example: lcpm <- cpm(y, log=TRUE, prior.count=3) because it reduces further the variability of low-count genes. I would have preferred that in the F1000Research paper that you cite, but, as you have not ...
written 11 hours ago by Gordon Smyth35k
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Answer: A: Queries related to limma package based analysis of masspectrometry data
... I don't recommend or use voom myself for MS data because there is no concept of sequencing depth for MS data. I instead analyse it much like microarray data, with the linear models fitted to the log-intensities. A critical decision is how you will impute missing values, when a peptide or protein is ...
written 2 days ago by Gordon Smyth35k
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Comment: C: limma barcodeplot(): calculation of enrichment score
... See also https://support.bioconductor.org/p/113501/ ...
written 2 days ago by Gordon Smyth35k
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Comment: C: PCA plot of variance stabilized transformation of normalized counts in limma
... I use "pairwise" unless the number of samples is very large. With a large number of samples, "pairwise" is quadratically slow so I switch to "common". ...
written 2 days ago by Gordon Smyth35k
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Answer: A: PCA plot of variance stabilized transformation of normalized counts in limma
... Yes, gene.selection="common" will make the MDS distance equivalent to PCA. To stabilize the variances for the MDS plot, use cpm() with prior.count=5. ...
written 3 days ago by Gordon Smyth35k
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Answer: A: Explanation of mroast results for specific biological processes and error with b
... Your questions 1) and 2) are biological questions rather than software questions, so you need to make these decisions yourself according to the scientific aims of your study. However, I would note that the genes associated with each GO Term are not constrained to all change in the same direction. Ge ...
written 6 days ago by Gordon Smyth35k
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Comment: C: Subscript error from TSS proximity function
... You could try nearestTSS() in the edgeR package, although it works on genomic loci rather than genomic intervals. ...
written 7 days ago by Gordon Smyth35k
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Comment: C: Limma Volcano Plot Highlight Top Genes by Color
... There's no need to print out the whole design matrix in this case, so I took it out to make your question a bit shorter and easier to read. ...
written 8 days ago by Gordon Smyth35k
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Answer: A: Limma Volcano Plot Highlight Top Genes by Color
... No, you haven't made a mistake. volcanoplot() doesn't give you a choice as to the color of the gene names on the plot. I will put add an argument to give you a choice in the next Bioconductor release. Continuing on James MacDonald's code example, you can easily add the gene names yourself, exactly ...
written 8 days ago by Gordon Smyth35k
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Answer: A: Perform limma based gene-set testing for a two-group comparison in a microarray
... 1) With 7 particular GO terms, I would use mroast. Why not? roast is designed for focused gene set tests. fry is an approximation to mroast but, with only 7 terms, you may as well use roast itself. For B) I would use camera. 2) Personally, I use alias2SymbolUsingNCBI() to convert gene symbols to E ...
written 11 days ago by Gordon Smyth35k

Latest awards to Gordon Smyth

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: Building linear model (age effect on gene expression)
Appreciated 6 weeks ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
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]
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to plot MD plot in limma
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?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Trouble with Tximport for edgeR
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: How barcode-plot enrichment is calculated?
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
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Analysis of pathways using edgeR
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: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Scholar 6 weeks ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Epic Question 10 weeks ago, created a question with more than 10,000 views. For EdgeR LogCpm and LogFC values calculation
Scholar 10 weeks ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Popular Question 10 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]
Popular Question 10 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?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For specifying filenames and celfile.path to ReadAffy()
Popular Question 10 weeks ago, created a question with more than 1,000 views. For edgeR - MDS plot
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to plot MD plot in limma
Scholar 10 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
Scholar 10 weeks ago, created an answer that has been accepted. For A: Building linear model (age effect on gene expression)

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