User: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth620
Reputation:
620
Status:
Trusted
Location:
Australia
Website:
http://www.statsci.org...
Scholar ID:
Google Scholar Page
Last seen:
5 hours ago
Joined:
4 years, 6 months ago
Email:
s****@wehi.edu.au

Joint Head of the 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, all part of the Bioconductor project.

Posts by Gordon Smyth

<prev • 37 results • page 1 of 4 • next >
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Answer: A: edgeR - DE with one disease sample vs. multiple control samples?
... There's no problem with this. edgeR handles unequal sample sizes automatically. It will simply estimate variability (i.e., the dispersion parameter) from the controls, where you do have replicates, and will then apply the same dispersion values to both cases and controls when conducting tests and co ...
written 4 days ago by Gordon Smyth620
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2
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Answer: A: (edgeR-related) DGElist error message 'Negative counts not allowed'.
... This is how I would do it: ``` library(edgeR) fc <- read.delim("counts_fcounts.txt", stringsAsFactors = FALSE) genes <- fc[,1:6] counts <- data.matrix(fc[,7:11]) row.names(counts) <- paste(genes$Geneid, genes$Start, genes$End, sep=".") group <- factor( c("FL","FL","HL","HL") ) y < ...
written 4 days ago by Gordon Smyth620
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2
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Answer: A: Query about gene ontology analysis in edgeR vs GSEA
... Yes, the `goana` and `kegga` functions test whether a high proportion of the genes for that GO term (or KEGG pathway) are DE. See `?goana`. ...
written 8 days ago by Gordon Smyth620
2
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Answer: A: error in read.maimages {limma}
... `read.maimages` requires all the Agilent data files to correspond to the same set of probes, with one row for each probe. It seems however that your files have different numbers of rows. ...
written 21 days ago by Gordon Smyth620
3
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Answer: A: Differential binding ChIP-seq/RNA-seq analysis
... csaw can handle any experimental design that edgeR can, i.e., it can handle any number of groups and any number of explanatory factors. To quote from the csaw User's Guide (page 41): > A generalized linear model (GLM) will be fitted to the counts for each window using the specified design [22]. ...
written 26 days ago by Gordon Smyth620
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Answer: A: Gene set analysis - minimum number of genes for moderated t statistics
... There is no minimum number of genes for a gene set. The moderation depends on all the genes in the whole data set (i.e., all the genes on the microarray or profiled by RNA-seq), not just on the genes in the test set. Moderation will give an advantage for any sized set. PS. The limma developers answ ...
written 4 weeks ago by Gordon Smyth620
2
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Answer: A: The optimal minMQS parameter in featureCounts for RNA-Seq quantification
... The question was also asked on Bioconductor https://support.bioconductor.org/p/117597/ and was answered by the developer. The recommendation is not to set a minMQS filter at all for RNA-seq analyses. ...
written 5 weeks ago by Gordon Smyth620
3
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Answer: A: Limma can make differential expression with just one case in one group?
... I think you may have misinterpreted limma's abilities slightly, because the sample size requirements for t-tests (with pooled variance) and for limma are essentially the same. Actually limma's sample size requirements are exactly the same as for anova. If I understand your question correctly, you h ...
written 5 weeks ago by Gordon Smyth620
2
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696
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Answer: A: How to do DMR analysis with BiSeq (for RRBS methylation data)?
... edgeR can be used for differential methylation analysis of RRBS data, including chromosomal level tests: https://f1000research.com/articles/6-2055/v2 edgeR estimates biological variation between replicate samples in a very effective way, and provides full linear model capabilities (multiple gro ...
written 6 weeks ago by Gordon Smyth620
2
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1
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286
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Answer: A: edger differential expression analysis error
... The basic problem is that you have asked `estimateCommonDisp` to estimate the negative binomial dispersion from just one gene, by passing just the 2nd row of data `y1[2,]` instead of the whole data object. Why would you do that? Since `y1` has only 2 columns, you are asking `estimateCommonDisp` to ...
written 6 weeks ago by Gordon Smyth620

Latest awards to Gordon Smyth

Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: Differential expression: replicates in one condition, no replicates in the other
Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: edgeR - DE with one disease sample vs. multiple control samples?
Scholar 4 days 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 days ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Autobiographer 4 weeks ago, has more than 80 characters in the information field of the user's profile.
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 7 weeks ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 9 weeks 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
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 3.3 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 4.1 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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