User: willj

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willj30
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France
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2 years, 2 months ago
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Posts by willj

<prev • 16 results • page 1 of 2 • next >
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Comment: C: affycoretools annotateEset problem using Clariom D arrays
... Great, thanks - it should have been obvious to me to check there. I note also for anyone else struggling with this that there is also some explanation of ChipDb here in an AnnotationDbi vignette: https://www.bioconductor.org/packages/devel/bioc/vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPacka ...
written 10 weeks ago by willj30
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Comment: C: affycoretools annotateEset problem using Clariom D arrays
... Thanks a lot James. By the way: is there some resource or document that would have pointed me to using your ChipDb without having to post a question here? i.e. something I should be keeping up-to-date with for future reference? ...
written 10 weeks ago by willj30
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affycoretools annotateEset problem using Clariom D arrays
... I'm coming up against an annotation mismatch error for probesets, when using annotateEset in the affycoretools package, and after having run rma using the oligo package. The following commands work fine: > rma.genes <- oligo::rma(rawData, target="core") Background correcting Normalizing Calc ...
affycoretools clariom written 10 weeks ago by willj30 • updated 10 weeks ago by James W. MacDonald45k
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Warning messages from diffSplice in Limma
... I have data from Affy Human exon arrays 1.0 ST, and I'm using the diffSplice function in Limma to detect differential splicing. I'm getting some warnings (see below) when I call diffSplice and I'd like to know if I should be concerned about them (results from topSplice and plotSplice look fine as fa ...
limma diffsplice written 7 months ago by willj30 • updated 7 months ago by Gordon Smyth32k
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Comment: C: Is it common to get all 0 values when running the randomForest step in GOexpress
... Great - thanks. ...
written 2.1 years ago by willj30
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Is it common to get all 0 values when running the randomForest step in GOexpress?
... The examples in the GOexpress vignette run correctly for me and I've now ran various subsets of my own data. The output looks generally sensible - identified GO terms are similar to those I find by other methods (e.g. limma differential expression followed by DAVID functional enrichment). However, I ...
goexpress written 2.1 years ago by willj30 • updated 2.1 years ago by kevin.rue200
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Comment: C: Correct use of arrayWeights alongside duplicateCorrelation for microarrays in Li
... Dear Ryan, thanks for your advice. I've repeated the analysis, this time using: corfit <- duplicateCorrelation(res.filt2, design, block = reps, weights=aw) The total number of differentially expressed genes is now more than doubled, but includes all of the DE genes identified in the previous ...
written 2.1 years ago by willj30
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Correct use of arrayWeights alongside duplicateCorrelation for microarrays in Limma?
... I'm trying to use arrayWeights for the experimental design described below which features technical replicates and the duplicateCorrelation function. I would greatly appreciate it if someone could confirm that what i'm doing is sensible. I want to determine differential expression for mutant v cont ...
limma duplicatecorrelation arrayweights written 2.1 years ago by willj30
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Comment: C: Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "det
... Mark - thanks very much for responding to my mail! And thanks to Gordon and you both for advice on how this will work with limma and lumi. ...
written 2.2 years ago by willj30
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Comment: C: Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "det
... Dear Gordon, thanks very much for explaining this about the GenomeStudio output and how it is interpreted by read.idat(), and for your advice on using your neqc function. I will try to find a way to contact the lumidat authors (edit: Mark Cowley commented below), but I do suggest that it was still g ...
written 2.2 years ago by willj30

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