User: willj

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willj30
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France
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5 days ago
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1 year, 8 months ago
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b********@hotmail.com

Posts by willj

<prev • 13 results • page 1 of 2 • next >
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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 5 weeks ago by willj30 • updated 5 weeks ago by Gordon Smyth30k
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Comment: C: Is it common to get all 0 values when running the randomForest step in GOexpress
... Great - thanks. ...
written 19 months 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 19 months ago by willj30 • updated 19 months 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 19 months 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 20 months 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 20 months 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 20 months ago by willj30
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Comment: C: Zero values for bead backgrounds (reading idat files using Illuminaio)
... Thanks Mike - this is very reassuring to know. Not being very familiar with idat files, I was worried that those zero values might impact on some downstream analyses. ...
written 20 months ago by willj30
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Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "detection_pval" given by GenomeStudio?
... I've ran several idat files of microarray data through lumidat, including the example idat files provided in the lumidat package. The "Detection" column always has it's greatest values (i.e. values at or close to 1) for the probes having the strongest signal strength. For example, below I paste outp ...
microarray illumina idat lumidat written 20 months ago by willj30 • updated 20 months ago by Mark Cowley400
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Comment: C: Zero values for bead backgrounds (reading idat files using Illuminaio)
... Hi Kasper - there is no problem with Illuminaio (both packages give me those zero values). However, lumidat has the advantage that it calculates a "detection" value, and feeds easily into Lumi. My main problem was getting from Illuminaio to Lumi. I still don't know why my idats have those zero value ...
written 20 months ago by willj30

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