Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth34k
Reputation:
34,110
Status:
Trusted
Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Website:
http://www.statsci.org...
Scholar ID:
Google Scholar Page
Last seen:
4 hours ago
Joined:
15 years, 6 months ago
Email:
s****@wehi.edu.au

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 • 3,339 results • page 1 of 334 • next >
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Answer: A: Building linear model (age effect on gene expression)
... library(ALL) library(limma) data(ALL) age <- pData(ALL)$age ALL2 <- ALL[, !is.na(age)] design <- model.matrix(~age) fit <- lmFit(ALL2, design) fit <- eBayes(fit, trend=TRUE) Then > topTable(fit, coef="age")             logFC AveExpr     t  P.Value adj.P.Val      B 40419_at  0. ...
written 4 hours ago by Gordon Smyth34k
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Answer: A: EdgeR Multivariate Analysis question
... Just following up Aaron's answer, the contrast you have given is a very powerful way of finding genes DE in Treatment B compared to the average of A and Controls. You will definitely not lose genes that you would have wanted to detect because of deviations between Control and Treatment. ...
written 9 hours ago by Gordon Smyth34k
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Answer: A: GSEA for RNA-seq analysis
... GSEA isn't a Bioconductor program. If you have questions about how to use it, then you should send them to the GSEA authors or to a GSEA forum. I will make a few comments though: I've never heard anyone claim that GSEApreranked is better than the standard GSEA methodology, so I don't know where y ...
written 1 day ago by Gordon Smyth34k
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Answer: A: I am unable to use Rsubread. Thank you in advance.
... Rsubread is only available for Unix and Mac. It is not available for Windows. ...
written 3 days ago by Gordon Smyth34k
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Answer: A: Compare in cont.matrix part
... Why not either cont.matrix <- makeContrasts(TGFbeta-Control, SSc–Control, levels=design) or cont.matrix <- makeContrasts(contrasts=c('TGFbeta-Control','SSc-Control'), levels=design)   It seems so me that reading help("makeContrasts") would answer your questions. There are usage examples ...
written 4 days ago by Gordon Smyth34k
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Answer: A: Limma weights, non-specific interactions
... From your description, it sounds like you are simply worried about probes with large variances. limma already downweights probes with large variances. Belinda Phipson and I have even written a paper specifically about how to deal with probes that have particularly large variances (which we call "hyp ...
written 4 days ago by Gordon Smyth34k
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Comment: C: Is number of rotations dependent on number of gene sets in mroast?
... What you say about multiple testing is right, but it seems to me that OP was asking a much more basic question. I've added a bit more detail to my reply. ...
written 5 days ago by Gordon Smyth34k
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Comment: C: Limma weights, non-specific interactions
... Yes, you understood what I was hinting at. Adding background arrays can be useful in some circumstances but is probably unnecessary. I'll write short answer. ...
written 5 days ago by Gordon Smyth34k
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Comment: C: Conditions for using Fry
... Yes, probably. I would myself use fry() over mroast(). ...
written 5 days ago by Gordon Smyth34k
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Comment: C: Tutor Wanted: help with R statistical analysis (must be familiar with Bioconduct
... My guess is that it is this course: https://moodle2.brandeis.edu/syllabus/142/142RBIF-111-1DL_1400020856.pdf ...
written 6 days ago by Gordon Smyth34k

Latest awards to Gordon Smyth

Scholar 10 weeks ago, created an answer that has been accepted. For A: Filtering Rna-seq counts
Scholar 10 weeks ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Popular Question 10 weeks ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: ANOVA-like test via treat() in limma
Scholar 10 weeks ago, created an answer that has been accepted. For A: Trouble with Tximport for edgeR
Scholar 10 weeks ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Popular Question 10 weeks ago, created a question with more than 1,000 views. For specifying filenames and celfile.path to ReadAffy()
Popular Question 10 weeks ago, created a question with more than 1,000 views. For edgeR - MDS plot
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Nanostring analysis with limma
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Analysis of pathways using edgeR
Scholar 10 weeks ago, created an answer that has been accepted. For A: Performing differential gene analysis on RT PCR experimental data
Scholar 10 weeks ago, created an answer that has been accepted. For A: Finding genes respond differently to treatment between many genotype comparison
Scholar 10 weeks ago, created an answer that has been accepted. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to plot MD plot in limma
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: using duplicateCorrelation with limma+voom for RNA-seq data
Scholar 10 weeks ago, created an answer that has been accepted. For A: Limma - how to manage huge differences in library sizes
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Using limma to model gene expression changes with age
Popular Question 10 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]
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 10 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 10 weeks ago, created an answer with at least 3 up-votes. For A: Trouble with Tximport for edgeR
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Scholar 3 months ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Scholar 3 months ago, created an answer that has been accepted. For A: How to plot MD plot in limma
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Analysis of pathways using edgeR

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