User: Julien Gagneur

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12 years, 7 months ago
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j*************@embl.de

Posts by Julien Gagneur

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Answer: A: IRanges problem: findOverlaps
... Indeed, Nico. interval_overlap() can moreover be strand-specific (on Genome_intervals_stranded objects). It also deals with so-called "inter-base" positions, i.e positions between two nucleotides to represent, for example, insertion points or restriction enzyme cutting sites. One thus can ask wheth ...
written 7.2 years ago by Julien Gagneur50
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gff files: how to tell if right-open interval convention used?
... Hi Simon, Karl and Herve, As Simon points out, the GFF3 format is quite ill-defined. When implementing readGff3() in genomeIntervals, we had to interpret the specifications. GFF3 allows zero-length features but there is no column to flag intervals as zero-length features. Have we missed something? ...
genomeintervals written 8.5 years ago by Julien Gagneur50 • updated 8.5 years ago by Hervé Pagès ♦♦ 14k
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Answer: A: stranded findOverlaps
... Dear Robert, for dealing with genomic intervals, you can also consider the genomeIntervals package. A class for stranded genomic intervals is available together with an interval overlap function that behaves in a strand-specific manner. Hope this helps, Julien ...
written 9.7 years ago by Julien Gagneur50
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Answer: A: Limma 2.9.10: "Amean" missing
... Thank you Gordon to clarify this point. In my context I am using it to extract mean log ratios, which I can get by other "means" :-) anyway. I understand that it would be a safer way to proceed. Best, Julien. Gordon Smyth wrote: > Dear Julien, > > The component 'Amean' in the output fr ...
written 12.6 years ago by Julien Gagneur50
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Limma 2.9.10: "Amean" missing
... Hi, I miss the Amean field in the output of eBayes() in limma 2.9.10 . It is there in limma 2.8.1 sample code: # Simulate gene expression data, # 6 microarrays and 100 genes with one gene differentially expressed set.seed(2004); invisible(runif(100)) M <- matrix(rnorm(100*6,sd=0.3),100,6) M ...
limma written 12.6 years ago by Julien Gagneur50 • updated 12.6 years ago by J.delasHeras@ed.ac.uk1.9k

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