User: sarah.williams1

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Location:
Melbourne, Monash University
Twitter:
@swbioinf
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5 months, 2 weeks ago
Joined:
3 years ago
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s**************@monash.edu

Posts by sarah.williams1

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Bioconductor support site search missing results?
... No worries, thanks Steve - as long as the issue is known. Maybe the search box should just quietly go away :) ...
written 6 months ago by sarah.williams120
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Bioconductor support site search missing results?
... Hi, Bioconductor support site question. I'm noticing some potential brokenness in the bioconductor search box. It seems to produce little to no results. e.g. seaching 'MAST' yeilds nothing, and 'limma' only 9 results. https://support.bioconductor.org/local/search/page/?q=MAST https://support.bioc ...
bioconductor support.bioconductor.org written 6 months ago by sarah.williams120 • updated 6 months ago by Steve Lianoglou12k
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Answer: A: Celaref error relating to MAST DE ananlysis
... Hi Hamid, apologies for missing this issue. Just adding this response for record, as per our email. Yes, that is an issue with the first version that you've got there (1.0.1) - sparse matrices weren't handled properly. A slight oversight! That has been fixed now though - so I'd suggest updating th ...
written 6 months ago by sarah.williams120
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Comment: C: Celaref error relating to MAST DE ananlysis
... see below, should be answer. ...
written 6 months ago by sarah.williams120
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Comment: C: HDF5Array Single cell experiment objects - can on-disk files change?
... Thanks for clarifying. Good to be sure :) ...
written 9 months ago by sarah.williams120
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HDF5Array Single cell experiment objects - can on-disk files change?
... Basic question about working with HDF5-backed / sparse/ delayedArray SingleCellExperiment objects: Because its stored on disk, does that mean operations on a large dataset could get realised live on the currently loaded data on disk? ie. if I do the following, sce <- loadHDF5SummarizedExpe ...
hdf5array written 10 months ago by sarah.williams120 • updated 10 months ago by Aaron Lun25k
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No gene hits in cameraPR - due to bug dropping statistic names?
... Hi, I have been using the pre-ranked cameraPR function for a custom ranking of genes for camera.  If I use the function as is, I get no hit genes at all: cameraPR(statistic=the_stat,index=Hs.c5.gene_name)[1:3,] NGenes Direction PValue FDR GO_REGULATI ...
limma camera written 2.3 years ago by sarah.williams120 • updated 2.3 years ago by Gordon Smyth39k
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VariantAnnotation error with readVcf after genotypeToSnpMatrix
... Hi, Struck an issue with running 'readVcf' function (in VariantAnnotation package) if it is called after genotypeToSnpMatrix(), or importing snpStats package. It works fine if called first. Simple workaround is to import SNPstats before VariantAnnotation - but might be worth a bug report? Examples ...
variantannotation written 3.1 years ago by sarah.williams120

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