User: Matthew Ritchie

gravatar for Matthew Ritchie
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Australia
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http://www.wehi.edu.au...
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mritchieau
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Posts by Matthew Ritchie

<prev • 73 results • page 2 of 8 • next >
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Comment: C: Appropriate explanation of the methodology behind arrayWeights function from lim
... Yes. Low quality (or high variability) could arise from a multitude of sources (e.g. the RNA may be degraded for a particular sample or tumor samples may be contaminated with normal cells to varying degrees, leading to increased variation etc. etc.) and the model has no way of knowing the precise so ...
written 2.1 years ago by Matthew Ritchie660
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Answer: A: edgeR:processAmplicons barcode match only 57% when it should be 100% -- I artifi
... Hi Anne, The processAmplicons function assumes that the sequences in your fastq file have a fixed structure - the locations of the sample indexes and shRNAs need to be fairly consistent, with the exact position specified by the user (some wobble is allowed via the allowShifting option, but not too ...
written 2.1 years ago by Matthew Ritchie660
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Answer: A: crlmm crossprod error, and missing files in annotation
... Hmm - not sure then. If you can provide a few examples IDAT files offline, I will take a closer look. ...
written 2.3 years ago by Matthew Ritchie660
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Answer: A: crlmm crossprod error, and missing files in annotation
... Are these OmniExpress24v1 chips referred to in your previous post? The OmniExpress12v1b package you're using above probably won't work for this platform as the probe IDs are likely to be different. We need to add a more informative error message here, but it generally arises when a chip type mismatc ...
written 2.3 years ago by Matthew Ritchie660
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Answer: A: Crlmm HumanOmniExpress-24v1 Annotation not available
... Hi Andrew, We don't currently support this platform, but are working towards an approach to handle data from any arbitrary platform without the need for a chip-specific package - we hope to make it available in the next release. Best wishes, Matt ...
written 2.3 years ago by Matthew Ritchie660
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Answer: A: read.idat manifest error
... Thanks for providing the example files. The problem was caused by a single probe that was listed in the manifest file but wasn't in the idat file. Have added a new 'tolerance' argument to read.idat in the devel version of limma (v 3.25.13, should be available over the next few days) to handle this. ...
written 2.4 years ago by Matthew Ritchie660
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Answer: A: read.idat manifest error
... If Mike's suggestion doesn't help, perhaps you can provide an idat file or two and the manifest you're using so that I can take a closer look. ...
written 2.4 years ago by Matthew Ritchie660
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News: Hands-on Bioconductor course, 7 Sept 2015, Tokyo
... A hands-on workshop on using Bioconductor for high-throughput sequence analysis will be presented by Dr Martin Morgan on 7th September 2015 at AIST in Tokyo. This event is a satellite workshop to GIW/InCoB2015 (http://www.jsbi.org/giw-incob2015/index.html). For further information, visit the works ...
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News: BioCAsia, 8 Sept 2015, Tokyo
... The first Bioconductor Asia-Pacific Developers' meeting will be held on 8th September 2015 in Tokyo as a satellite event to GIW/InCoB2015 (http://www.jsbi.org/giw-incob2015/index.html). For more information, visit the meeting website    http://www.bioconductor.org/help/course-materials/2015/BiocAs ...
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Answer: A: reading .idat files using genotype.Illumina in crlmm
... Hi Tao, No, you don't need to provide a sample sheet - it is optional. Cheers, Matt ...
written 2.4 years ago by Matthew Ritchie660

Latest awards to Matthew Ritchie

Scholar 2.3 years ago, created an answer that has been accepted. For A: Crlmm HumanOmniExpress-24v1 Annotation not available

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