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Moderator: Gordon Smyth

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Gordon Smyth36k
Reputation:
36,230
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Trusted
Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Website:
http://www.statsci.org...
Scholar ID:
Google Scholar Page
Last seen:
5 hours ago
Joined:
16 years ago
Email:
s****@wehi.edu.au

Joint Head of 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.

Posts by Gordon Smyth

<prev • 3,543 results • page 1 of 355 • next >
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Comment: C: KEGGREST mapping between genes and pathways
... The ID with "t" is the transcript ID. The ID with "g" is the locus ID. See for example the gene annotation file you can download from here: https://rapdb.dna.affrc.go.jp/download/irgsp1.html ...
written 15 hours ago by Gordon Smyth36k
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Answer: A: Making sense out of makeContrasts and using coefficents for contrasts
... You are trying to combine separate contrasts into one contrast, but that can't be done. You do have to keep all the separate comparisons between treatments at each time-point as separate contrasts. So you need: ``` con<- makeContrasts( T6SPLDvsLD = T6.SPLD.FW - T6.LD.FW, T5SPLDvsLD = T5. ...
written 17 hours ago by Gordon Smyth36k
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Answer: A: Using RUVSeq RUVs() to perform batch correction using technical replicates
... I am having trouble making sense of your question because your PCA plots show a clear separation of the samples into two groups, but the groups are not associated with any of the variables in your experiment and you don't comment on this. The groups I am referring to you are the obvious groups at t ...
written 19 hours ago by Gordon Smyth36k
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Comment: C: RNA-seq batch correction using technical replicates profiled across batches
... No, batch is not perfectly confounded with condition, because condition B is in both batches and, more than that, the exact same samples are in both batches. Presumably, the whole purpose of repeating the condition B samples was in order to deconfound the batches. What I have suggested to you does ...
written 1 day ago by Gordon Smyth36k
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Comment: C: KEGGREST mapping between genes and pathways
... You'd have to ask KEGG rather than me. Presumably they are transcript version numbers. It might be fine to remove them. ...
written 1 day ago by Gordon Smyth36k
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Answer: A: RNA-seq batch correction using technical replicates profiled across batches
... I would use limma for an experiment like this. I would analyse all the samples together, including a batch effect term in the linear model and using `duplicateCorrelation()` to link the technical replicates of the same samples. (The duplicateCorrelation `block` variable is the same as the sample ID. ...
written 1 day ago by Gordon Smyth36k
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Answer: A: KEGGREST mapping between genes and pathways
... You don't need to convert your IDs. KEGG already provides a mapping between the Japanese rice genome pathways and RAPIDs. For example, you can use the `kegga` function in the limma package with `species.KEGG="dosa"` and it will use RAPIDs directly. To see which RAPIDs KEGG is using, have a look at ...
written 1 day ago by Gordon Smyth36k
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Answer: A: classifyTestsP vs topTable
... Please use `decideTests` instead of `classifyTestsP`. The latter does not adjust for multiple testing across genes and is not intended to be called directly by users. ...
written 1 day ago by Gordon Smyth36k
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Answer: A: Limma p-values, fdr and classifyTests
... Just use `decideTests` instead of `classifyTests`. The latter does not adjust for multiple testing across genes and is not intended to be called directly by users (as the help page says). `decideTests` does everything and calls the other functions as needed. ...
written 1 day ago by Gordon Smyth36k
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Answer: A: Limma FDR and p.value
... I think you are assuming that `classifyTestsP()` adjusts for multiple testing across genes. Actually it adjusts only across contrasts, i.e., across rows rather than down columns. As the help says *"The adjustment for multiple testing is across the contrasts rather than the more usual control acro ...
written 1 day ago by Gordon Smyth36k

Latest awards to Gordon Smyth

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Using write.table with output from topTags [was: report a possible bug of edgeR]
Scholar 5 weeks ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How barcode-plot enrichment is calculated?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Genbank to Unigene IDs
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Using write.table with output from topTags [was: report a possible bug of edgeR]
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Removing continuous covariate effects in limma analysis
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: How barcode-plot enrichment is calculated?
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Removing continuous covariate effects in limma analysis
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: How barcode-plot enrichment is calculated?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For specifying filenames and celfile.path to ReadAffy()
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: ANOVA-like test via treat() in limma
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How barcode-plot enrichment is calculated?
Scholar 11 weeks ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Appreciated 3 months ago, created a post with more than 5 votes. For A: How barcode-plot enrichment is calculated?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Removing continuous covariate effects in limma analysis
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How barcode-plot enrichment is calculated?
Scholar 3 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Scholar 3 months ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Popular Question 3 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 3 months ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Epic Question 3 months ago, created a question with more than 10,000 views. For limma moderated t-statistics and B-statistics
Popular Question 4 months ago, created a question with more than 1,000 views. For How do I find up and down regulated genes for each contrast in LIMMA?
Popular Question 4 months ago, created a question with more than 1,000 views. For rcmd check does not recognize generic function definitions

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