Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth32k
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31,710
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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:
1 day, 21 hours ago
Joined:
14 years, 9 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

<prev • 3,062 results • page 2 of 307 • next >
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Comment: C: Using R for EnrichR analysis
... An alternative would be to use the Enrichr web interface. ...
written 17 days ago by Gordon Smyth32k
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Answer: A: Limma Ebayes on SILAC data
... I am not familiar with SILAC ratiometric data but, if it produces log-expression ratios, then you could analyse the results like those from two colour microarrays. Your data appears to be similar to the design considered in Section 11.2.1 of the limma User's Guide. In that case, you don't need to cr ...
written 17 days ago by Gordon Smyth32k
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Comment: C: Using R for EnrichR analysis
... What do you mean by "EnrichR"? As far as I know, there is no statistical method or software package of that name and capitalization as far as I know. If you just mean gene ontology or KEGG pathways analysis of DE genes, you could look at the goana() or kegga() functions of the limma package. These ...
written 17 days ago by Gordon Smyth32k
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Answer: A: Venndigram of LIMMA decideTests() function for more than 5 sets
... I don't have any plans to offer Venn diagrams in limma for more than 5 sets, because I don't find Venn diagrams with more than 5 sets to be at all useful. They seem far too contrived to help with interpretation. With so many sets, just looking at the tabular output from vennCounts() is better. Alter ...
written 18 days ago by Gordon Smyth32k
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Answer: A: How to take mean from specific column
... The avearrays() function in the limma package does what you want. For example, if the replicates you want to average are side by side, then ID <- rep(1:104, each=2) ReducedExprMatrix <- avearrays(ExprMatrix, ID) In general, columns with the same ID will be averaged. ...
written 18 days ago by Gordon Smyth32k
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Comment: C: Upgrade to 3.6 - can't seem to get past Bioconductor 3.5
... My mistake -- now fine. ...
written 21 days ago by Gordon Smyth32k
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Comment: C: Upgrade to 3.6 - can't seem to get past Bioconductor 3.5
... It's still not working correctly. ...
written 21 days ago by Gordon Smyth32k
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Answer: A: edgeR - problem with glmQLFTest()
... Thanks David. I have committed a fix to edgeR 3.20.1 for Bioconductor 3.6. ...
written 21 days ago by Gordon Smyth32k
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Comment: C: edgeR - problem with glmQLFTest()
... I've edited the gist URL so that it shows as a link instead of inserting the whole dataset. ...
written 21 days ago by Gordon Smyth32k
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Comment: C: Bioconductor 3.6 release: 3.6 branch created
... The git repositories are updated, but it seems that BiocInstaller::biocLite isn't working correctly yet for Bioc 3.6. I guess I'm jumping the gun and should wait for tomorrow.​ ...
written 21 days ago by Gordon Smyth32k

Latest awards to Gordon Smyth

Scholar 4 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Appreciated 4 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Popular Question 5 months ago, created a question with more than 1,000 views. For Limma - RNA-Seq DE genes - Quantile normalized log transformed RPKM data
Popular Question 6 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 6 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 6 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tes
Teacher 6 months 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 7 months ago, created a question with more than 1,000 views. For Filtering is not recommended with LIMMA?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Confidence intervals on edgeR logFC
Scholar 7 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Appreciated 7 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Scholar 7 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 7 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Commentator 7 months 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 months ago, created a comment with at least 3 up-votes. For C: How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 8 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 8 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 8 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 8 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 8 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet

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