Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth33k
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32,860
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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:
2 hours ago
Joined:
15 years, 2 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

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Comment: C: Limma model for paired and pool together
... Agreed, the paired model ~Cell + Donor is correct here. There's no heteroskedasticity issue here though because any variation between Donors is being removed by the paired model. The analysis of variation is purely within Donor, so the degree of variability in baseline expression from one Donor to ...
written 1 day ago by Gordon Smyth33k
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Answer: A: Design/contrast matrix for Multivariate experimental design in limma
... Making the design matrix is easy. If you are doing a classical two-color analysis of log-ratios, then you just give the Cy3 and Cy5 columns to modelMatrix() and it forms the design matrix for you. If you doing a separate channel analysis using lmscFit() as described here: https://bmcbioinformatics. ...
written 3 days ago by Gordon Smyth33k
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Comment: C: read counts for gene families
... For an edgeR analysis, fry() is quicker and better than roast(). It's actually equivalent to using roast() with nrot=Inf. ...
written 4 days ago by Gordon Smyth33k
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Answer: A: read counts for gene families
... As Ryan has already pointed out, you don't need to add anything, counts or otherwise. Just do a gene set test for your family of genes. Suppose your DGEList object is dge, and suppose you have an annotation column called "Symbol". Then Family <- c("A1","A2","A3") fry(dge, index=Family, design= ...
written 4 days ago by Gordon Smyth33k
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Answer: A: Error in ebayes in limma when analyzing GTEx data
... The whole approach of including 'subject' in the design matrix is inappropriate here. You are wanting to test for a difference between two groups of subjects (cvd vs non-cvd) so it makes no sense to correct the data for subject differences first. That would remove the cvd vs non-cvd differences toge ...
written 6 days ago by Gordon Smyth33k
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Answer: A: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
... There's no need for a special function in edgeR because it's easy using ordinary R programming: tab <- as.data.frame(topTags( ... )) tab[ tab$logFC > 0, ] tab[ tab$logFC < 0, ]   ...
written 7 days ago by Gordon Smyth33k
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Comment: C: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
... Hello fawazfebin! Questions similar to yours can already be found at: Separate listing of up-regulated and down-regulated genes in edgeR DGE results. We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us wh ...
written 7 days ago by Gordon Smyth33k
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Answer: A: box plot of idat files
... You don't say what you're are trying to make a boxplot of, but perhaps you are wanting to do something like this: Before neqc: logExpr <- log2(data$E) boxplot( as.data.frame(logExpr) ) After neqc: boxplot( as.data.frame(datanorm$E) ) These commands make boxplots of the log2-expression val ...
written 8 days ago by Gordon Smyth33k
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Comment: C: Differential expression testing for groups with unequal variances/dispersions?
... This question was answered 5 years ago, see here:       https://support.bioconductor.org/p/52866/ You could also use the limma function voomWithQualityWeights(). ...
written 9 days ago by Gordon Smyth33k
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Comment: C: Processing agilent data by limma
... For some reason, the exon arrays have been hybridized using the Cy5 (red) channel instead of Cy3 (green). To read them, you'll have to use a trick to tell read.maimages() to use the red channel only: x <- read.maimages(files, source="agilent", green.only=TRUE,   columns=list(G= ...
written 10 days ago by Gordon Smyth33k

Latest awards to Gordon Smyth

Scholar 9 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Appreciated 9 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Popular Question 10 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 11 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 11 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 11 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Teacher 11 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 11 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 12 months ago, created a question with more than 1,000 views. For Filtering is not recommended with LIMMA?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Confidence intervals on edgeR logFC
Scholar 12 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Appreciated 12 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Scholar 12 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 12 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Commentator 12 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 12 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 13 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 13 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 13 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 13 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 13 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 13 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet

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