User: Tim Rayner

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Tim Rayner270
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Posts by Tim Rayner

<prev • 27 results • page 1 of 3 • next >
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rtracklayer import.gff3 mangling scores
... Hi, I've just run into what I think is a bug in the rtracklayer import.gff3 function (v1.16.1). If I import a GFF3 containing scores while stringsAsFactors=TRUE, the resulting scores are mangled. I haven't confirmed it, but I suspect the values are being converted to a factor upon import and then c ...
snp rtracklayer written 5.6 years ago by Tim Rayner270 • updated 5.6 years ago by Michael Lawrence9.9k
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Answer: A: RE : Error in intgroup of arrayQualityMetrics package
... Hi Sonal, You could try rearranging pData(eset) so that the "Tissue" column is the first column, or within the first few columns. There's some preprocessing code in the arrayQualityMetrics:::cleanUpPhenoData function which limits the number of columns which will be carried forward into the QC (maxc ...
written 5.7 years ago by Tim Rayner270
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Comment: C: GenomicFeatures makeTranscriptDbFromBiomart failure
... Hi Herv?, Thanks very much for fixing this. I can confirm that GenomicFeatures 1.6.5 works on our Linux server. Interestingly, the warnings about duplicated levels have also now disappeared in that case. I initially ran into a new problem with GenomicFeatures 1.6.6 (see the bug report and session ...
written 6.1 years ago by Tim Rayner270
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Comment: C: GenomicFeatures makeTranscriptDbFromBiomart failure
... Hi Marc, Thanks very much for looking into this, and also to Michael for providing the patch. I've upgraded my GRanges package and the code now runs with a couple of warnings: > txdb.Hs2 <- makeTranscriptDbFromBiomart(biomart='ensembl', dataset='hsapiens_gene_ensembl') Download and preproces ...
written 6.3 years ago by Tim Rayner270
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GenomicFeatures makeTranscriptDbFromBiomart failure
... Hi, I'm trying to make a TranscriptDb from the Ensembl human Biomart, but I've run into a problem. As shown below, the equivalent operation for the mouse Biomart works fine: > # Mouse TranscriptDb created without a hitch: > txdb.Mm <- makeTranscriptDbFromBiomart(biomart='ensembl', dataset ...
transcriptdb biomart written 6.3 years ago by Tim Rayner270 • updated 6.3 years ago by Michael Lawrence9.9k
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edd deprecation
... Hi, I note from the .onLoad() message in the current release package for edd (v.1.32.0) that this package will not be supported after the current Bioconductor release. Are there any suggested approaches to replacing the functionality of this package in our analysis pipelines? My apologies if I have ...
written 6.3 years ago by Tim Rayner270 • updated 6.3 years ago by Vincent J. Carey, Jr.6.2k
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arrayQualityMetrics and NChannelSets
... Hi, Just a quick note to observe that the current stable version of arrayQualityMetrics seems to have a problem with NChannelSet objects: > nc NChannelSet (storageMode: lockedEnvironment) assayData: 1178100 features, 50 samples element names: exprs protocolData rowNames: GWAS16.10_160_CD16. ...
written 6.4 years ago by Tim Rayner270 • updated 6.4 years ago by Wolfgang Huber13k
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Answer: A: lumi, Illumina Methylation 450k, and robust methylation calls
... Hi Pietro, You can replace the call to .initialGammaEstimation() with lumi:::.initialGammaEstimation(). It's a fairly shameless hack which may well fail to work with subsequent versions of lumi, but with any luck that point is moot. Having looked at our results I'd say I'm pretty confident that the ...
written 6.6 years ago by Tim Rayner270
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lumi, Illumina Methylation 450k, and robust methylation calls
... Hi, I have recently started to use the lumi package to analyse some Illumina Human Methylation 450k data, and I have run into some problems which seem to revolve around division by zero in the gammaFitEM() function. I have adjusted the colour balance and quantile normalised as suggested in the vign ...
lumi written 6.7 years ago by Tim Rayner270 • updated 6.7 years ago by Ina Hoeschele610
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arrayQualityMetrics::aqm.nuse and GeneST
... Hi, I think I've run into a bug on the latest arrayQualityMetrics release. I'm running the function on an AffyBatch object created from HuGene ST 1.0 CEL files which I've tested with previous versions of arrayQualityMetrics without any problems: > arrayQualityMetrics(cd8, outdir='canonical_qc') ...
arrayqualitymetrics written 7.3 years ago by Tim Rayner270 • updated 7.3 years ago by Wolfgang Huber13k

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