Moderator: Gordon Smyth

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Gordon Smyth33k
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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 change sample names in featureCounts or edgeR
... Continuing the code I gave you previously ( https://support.bioconductor.org/p/109969 ) rc <- featureCounts(...) y <- DGEList(rc$counts) colnames(y) <- paste0("Chuong",553:656)   ...
written 1 day ago by Gordon Smyth33k
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Comment: C: Problem with write.fit function
... That's because write.fit is writing out the rownames, and the rownames don't have a column heading. If you don't want to write out rownames, use row.names=FALSE in your call to write.fit. ...
written 1 day ago by Gordon Smyth33k
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Answer: A: Genes listed in GO categories
... Dear Fernanda, Actually goseq is using up-to-date annotation. Here is what's happening. If you supply your own gene2cat annotation, then goseq will use that. If you don't, then goseq uses the GO-gene associations provided in the relevant Bioconductor organism package, in this case org.Bt.eg.db. Th ...
written 1 day ago by Gordon Smyth33k
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Comment: C: Genes listed in GO categories
... I agree that sticking to native gene ids is desirable if one can do it, and I agree that the goseq documentation gives the impression of being Ensembl orientated whereas it actually uses the Bioc organism packages by default. But do you really mean to say that mapping gene Ids is never a sensible t ...
written 3 days ago by Gordon Smyth33k
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Answer: A: Handling pseudogenes in RNA-seq
... This forum is to help you with Bioconductor software, but neither STAR nor zUMIs are Bioconductor packages. You need to send your question to the zUMIs authors, for example on their github issues page. ...
written 3 days ago by Gordon Smyth33k
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Comment: C: Genes listed in GO categories
... James, I am not a goseq author and I haven't examined the code, but it seems to me that goseq is most likely doing the right thing. You compute a vector huh2 of over 500 gene ids, but only 184 of those ids can be mapped to GO terms using the organism package. The entries that are NA in gene2cat but ...
written 4 days ago by Gordon Smyth33k
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Answer: A: How edgeR reads an R List object produced by featureCounts
... Feature counts just produces an R object (a simple list) so there is need to read anything. It doesn't write anything to disk. You just use the object directly in your R session, for example fc <- featureCounts(...) y <- DGEList(fc$counts) See for example the section called "Quantifying Rea ...
written 5 days ago by Gordon Smyth33k
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Answer: A: How i can get a list of KEGG pathways and its list of genes?
... > library(limma) > tab <- getGeneKEGGLinks(species="hsa") > tab$Symbol <- mapIds(org.Hs.eg.db, tab$GeneID,   column="SYMBOL", keytype="ENTREZID") > head(tab)   GeneID     PathwayID Symbol 1  10327 path:hsa00010 AKR1A1 2    124 path:hsa00010  ADH1A 3    125 pat ...
written 7 days ago by Gordon Smyth33k
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Answer: A: Removing batch effect from gene expression before Limma linear modelling
... No, that approach is not correct, as has been pointed out before on this support site. You need to include the batch factor in the linear model rather than attempt to remove the batch before hand. The help page for removeBatchEffect() says that it is intended to prepare data for plotting, not for i ...
written 8 days ago by Gordon Smyth33k
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Comment: C: edgeR for continuous independent variables
... I don't have time to go through your code in detail, but it isn't correct to filter by standard deviation. You should only filter by mean. ...
written 8 days ago by Gordon Smyth33k

Latest awards to Gordon Smyth

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Analysis of pathways using edgeR
Scholar 4 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 4 weeks ago, created an answer that has been accepted. For A: How to plot MD plot in limma
Teacher 4 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 4 weeks ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: RNA-Seq, generate batch-free count matrix
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please share me your helpful comments with edgeR analysis without replicate
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Do the outputs of Limma's competitive gene set methods (camera, romer) require a
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: using duplicateCorrelation with limma+voom for RNA-seq data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Differential expression of RNA-seq data using limma and voom()
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Test whether expression levels of two gene sets are significantly different
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Diffbind: edgeR or DESeq2 ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: how to use "non-standard" species for KEGG / GO analysis in limma?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Fit a multinomial to RNA-seq count data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: vooma lm.fit versus voom lmFit
Teacher 11 months ago, created an answer with at least 3 up-votes. For Differences between limma voom E values and edgeR cpm values?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: goana limma- extract list of DE genes and genes in the enriched GO terms?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.
Teacher 11 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
Student 11 months ago, asked a question with at least 3 up-votes. For non-integer counts for edgeR

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