Moderator: Gordon Smyth

gravatar for Gordon Smyth
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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Head of Bioinformatics Division at the Walter and Eliza Hall Institute of Medical Research

Posts by Gordon Smyth

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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 3 days ago by Gordon Smyth30k
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... OK, good luck. Personally I would realign all the FastQ files from scratch to make them compatible. Or at very least, quantify both sets of BAM files to the same gene annotation. ...
written 18 days ago by Gordon Smyth30k
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Answer: A: Subject: Strange glitch in Voom curve resulting from batch effects
... I suspect that there is a major difference in protocols or processing between the batches. A first step to exploring this would be to identify which genes are most DE between the batches (for the same group). However you cannot use the first batch anyway. Batches always need to contain samples for ...
written 19 days ago by Gordon Smyth30k
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Comment: C: beadsummary example- Analysing data from GEO
... People would have a better chance of helping you if you told us which GEO series you're trying to read and you gave all the code up to the error message. ...
written 23 days ago by Gordon Smyth30k
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Answer: A: Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tes
... It's really much simpler than that! An anova approach will do exactly what you want, finding genes that are different between individuals but consistent within individuals. If you didn't have a batch effect, then this would work: Individual <- factor(Dems$Individual) design <- model.matrix(~ ...
written 29 days ago by Gordon Smyth30k
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Answer: A: Problem Installing limma package
... Bioconductor hasn't been officially released yet for R 3.4.0 -- that will happen within the next 24 hours (April 25 American time). In the meantime, you're trying to install the developmental version. The reason why you've run into a problem is probably that there was an error in limma 3.31.21 whic ...
written 29 days ago by Gordon Smyth30k
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Answer: A: Warning messages from diffSplice in Limma
... Yes, you should be worried by the unlabelled probesets. diffSplice() assumes that you know which gene each exon belongs to. You have 787k exons in total but 505k of these have no gene identifier. So you do need to fix this basic data problem before proceeding. Is there no annotation as to which exon ...
written 4 weeks ago by Gordon Smyth30k
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Comment: C: GOseq: count bias correction variations?
... No, it isn't meaningful. Salmon is good at what it does, but the biases it adjusts for don't help at all with a goseq analysis. The count bias that goseq corrects for doesn't have anything to do with unequal library sizes or voom or normalization methods. goseq is concerned with the fact that the d ...
written 5 weeks ago by Gordon Smyth30k
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Comment: C: GOseq: count bias correction variations?
... If you have a measure of effective gene length from software like Rsubread or tximport, then you can easily pass it to GOseq or goana(). You've always been able to do that. There is no need to use the gene length database that comes with GOseq in that case. If you want to discuss more about gene le ...
written 5 weeks ago by Gordon Smyth30k
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Answer: A: GOseq: count bias correction variations?
... First, let me say that I always find the term "normalized counts" quite unhelpful, because people frequently have different things in mind when they use this expression. It is not a well-defined term. Normalized for library size? Normalized by TMM factors? RPKM? TPM? Who knows! I always ask people t ...
written 5 weeks ago by Gordon Smyth30k

Latest awards to Gordon Smyth

Popular Question 13 days ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tes
Teacher 28 days 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 4 weeks ago, created a question with more than 1,000 views. For Filtering is not recommended with LIMMA?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Confidence intervals on edgeR logFC
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 5 weeks ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Appreciated 6 weeks ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Scholar 6 weeks ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 7 weeks ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Commentator 7 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 7 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 9 weeks ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 10 weeks ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 10 weeks 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 10 weeks ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 11 weeks ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 11 weeks ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 12 weeks ago, created a question with more than 1,000 views. For File format for single channel analysis of Agilent microarray data with Limma?
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: limma; Only fit list of certain genes/ filter eSet
Great Question 3 months ago, created a question with more than 5,000 views. For EdgeR LogCpm and LogFC values calculation
Scholar 3 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet

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