Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth29k
Reputation:
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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 minutes ago
Joined:
13 years, 11 months ago
Email:
s****@wehi.edu.au

Head of Bioinformatics Division at the Walter and Eliza Hall Institute of Medical Research

Posts by Gordon Smyth

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Answer: A: error in Limma analysis - estimated df (df.0) for prior value of variance (s2.po
... Just to add to Aaron's answer, this is not an error from limma. If all the variances in your experiment appear to be the similar within sampling variability, then limma will treat them as the same and will pool all the protein-wise variances to get a combined variance estimate. This is why you have ...
written 8 minutes ago by Gordon Smyth29k
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Answer: A: Accessing KEGG (errors w/ KEGGREST)
... You can access KEGG using basic R commands. For example: > Pathways <- read.table("http://rest.kegg.jp/list/pathway/hsa", quote="", sep="\t") > head(Pathways)              V1                                                              V2 1 path:hsa00010             Glycolysis / Gluconeog ...
written 17 hours ago by Gordon Smyth29k
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Answer: A: One replicate (one-color OR two-color) is enough to use Limma?
... Dear Kevin, I have to correct one of the statements you made: limma does not "give wrong information" if there are no replicates. What it actually does is to refuse to estimate variances or to compute p-values when there are no replicates. In that case it simply returns log-fold-changes. In other w ...
written 1 day ago by Gordon Smyth29k
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Comment: C: searching for edgeR version 2.2.6
... Why do you want to install edgeR 2.2.6? That seems a very strange thing indeed to do. ...
written 1 day ago by Gordon Smyth29k
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Answer: A: Difficulty for analysis of GSE7864
... You can't analyse this data using limma because there is no replication. If you want to find probes with a 2-fold change in any particular sample, sample j say, simply select probes with abs(exprs(eset)[,j]) > log10(2). ...
written 2 days ago by Gordon Smyth29k
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Answer: A: Aggregate read counts by non-uniform overlapping sliding windows
... In terms of speed, counting everything fresh using featureCounts will be much faster than than anything else you might do. It's a very fast function. As Aaron has indicated, it is also easier to get it right that way: to be sure that you're counting the correct reads. ...
written 4 days ago by Gordon Smyth29k
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Comment: C: LIMMA and Agilent single color
... Dear Amal, You've posted an "answer", but really you are asking a new question rather than answering the above question by Patrick de Boever. Your question apparently relates to gene set testing in limma rather than to any issue raised by Patrick, so please post your query to Bioconductor as a fres ...
written 4 days ago by Gordon Smyth29k
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Answer: A: LIMMA and Agilent single color
... This question is answered here: https://support.bioconductor.org/p/37041/ ...
written 4 days ago by Gordon Smyth29k
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... No, there is no typo. The y-values are approximately log2(count+1) so, if I want the counts to be >10, then I need y > log2(10+1). Obviously you can do other analyses for MSI status and so on, but a complete analysis is your job, not mine. ...
written 4 days ago by Gordon Smyth29k
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... You can filter genes using the same sort of common sense considerations that we always use for differential expression analyses. I have edited my answer to illustrate this. ...
written 5 days ago by Gordon Smyth29k

Latest awards to Gordon Smyth

Teacher 9 months ago, created an answer with at least 3 up-votes. For Differences between limma voom E values and edgeR cpm values?
Scholar 9 months ago, created an answer that has been accepted. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Scholar 9 months ago, created an answer that has been accepted. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Appreciated 9 months ago, created a post with more than 5 votes. For A: Confidence intervals on edgeR logFC
Teacher 9 months ago, created an answer with at least 3 up-votes. For Differences between limma voom E values and edgeR cpm values?
Teacher 9 months ago, created an answer with at least 3 up-votes. For Differences between limma voom E values and edgeR cpm values?
Appreciated 9 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Scholar 10 months ago, created an answer that has been accepted. 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: Diffbind: edgeR or DESeq2 ?
Good Question 10 months ago, asked a question that was upvoted at least 5 times. For BH vs BY in p.adjust + FDR interpretation
Popular Question 10 months ago, created a question with more than 1,000 views. For How does Limma calculate the log2 fold change?
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: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Scholar 10 months ago, created an answer that has been accepted. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Scholar 11 months ago, created an answer that has been accepted. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Teacher 11 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 11 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 11 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
Scholar 11 months ago, created an answer that has been accepted. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Scholar 11 months ago, created an answer that has been accepted. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Teacher 11 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
Scholar 11 months ago, created an answer that has been accepted. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Teacher 11 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 11 months ago, created an answer with at least 3 up-votes. For A: how to use "non-standard" species for KEGG / GO analysis in limma?
Scholar 12 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps

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