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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http://www.statsci.org...
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Google Scholar Page
Last seen:
22 hours ago
Joined:
14 years, 4 months ago
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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: Identification of DEGs through limma analysis
... If you read the help page for decideTests(), it will answer all your questions. The default behaviour of decideTests() is to choose genes using an FDR cutoff of 0.05. The default settings are for p.value = 0.05 and adjust = "BH", so the first code option you give in your question is just the same a ...
written 22 hours ago by Gordon Smyth30k
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Comment: C: How to perform ANOVA to calculate differential gene expression with three catego
... You say you have a "good amount of experience" with DE analysis. What software have you used to do these analyses? I am wondering why anova causes such a special difficulty. ...
written 1 day ago by Gordon Smyth30k
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Answer: A: How to perform ANOVA to calculate differential gene expression with three catego
... The limma User's Guide covers this. It's very common analysis. ...
written 1 day ago by Gordon Smyth30k
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Comment: C: Trouble with DESeq2, edgeR, and limma not accepting zeros in input
... You say "have to look through the entire data" as if this is a difficult thing. Really you can just type anyNA(cts) ...
written 10 days ago by Gordon Smyth30k
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Answer: A: Trouble with DESeq2, edgeR, and limma not accepting zeros in input
... None of these software programs have any difficulty with zeros, so that is not the problem. There is one exception: you cannot reasonably have a entire sample with nothing in it at all, i.e., a column that is entirely zero. However even that would not lead to the errors you are seeing. Rows (genes) ...
written 13 days ago by Gordon Smyth30k
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Answer: A: Limma - RNA-Seq DE genes - Quantile normalized log transformed RPKM data
... Dear Avinash, Briefly, you have used design <- model.matrix(~0+Group) when you needed design <- model.matrix(~Group) However, I do not recommend a limma analysis of RPKM values, because it does not respect the mean-variance relationship inherent in the count data. Nicole Cloonan's excel ...
written 15 days ago by Gordon Smyth30k
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Comment: C: exon counting with featureCounts
... You should add "Rsubread" as a tag to your question, otherwise the Rsubread author might not be alerted to your question. ...
written 18 days ago by Gordon Smyth30k
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Answer: A: Samples without pair in paired design experiment
... If you use any of the negative binomial packages (like DESeq2 or edgeR) then you'll simply have to omit the samples without a pair. Actually it makes no difference whether you explicitly omit them or not, because the linear modelling approach implemented in those packages will have the effect of rem ...
written 21 days ago by Gordon Smyth30k
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Answer: A: miRNA differential expression analysis
... Do you mean  A vs (B+C)/2? That would compare A to the average of B & C, and would be done by contrast = c(1,-1/2,-1/2,0) if there are four groups in total. A vs (B+C+D)/3 would be done by contrast = c(1,-1/3,-1/3,-1/3). ...
written 29 days ago by Gordon Smyth30k
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Answer: A: How to retrieve all logFCs fom "glmQLFTest()" output-edgeR?
... You're apparently using a version of edgeR and Bioconductor that is not the latest. Try running R 3.4.0 and installing the latest version of  edgeR. ...
written 4 weeks ago by Gordon Smyth30k

Latest awards to Gordon Smyth

Popular Question 16 days ago, created a question with more than 1,000 views. For Limma - RNA-Seq DE genes - Quantile normalized log transformed RPKM data
Scholar 29 days ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 29 days ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tes
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tes
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Filtering is not recommended with LIMMA?
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Confidence intervals on edgeR logFC
Scholar 9 weeks ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Appreciated 10 weeks ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Scholar 11 weeks ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 11 weeks ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 3 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: seeking a paper or journal review about repeated multiple testing for Biological
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 3 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 3 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 3 months ago, created a question with more than 1,000 views. For File format for single channel analysis of Agilent microarray data with Limma?
Scholar 4 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet

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