User: Matthew Ritchie

gravatar for Matthew Ritchie
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690
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Australia
Website:
http://www.wehi.edu.au...
Twitter:
mritchieau
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Google Scholar Page
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1 week, 6 days ago
Joined:
13 years, 12 months ago
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Posts by Matthew Ritchie

<prev • 76 results • page 1 of 8 • next >
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Answer: A: voomWithQualityWeights, design and weights
... Your approach sounds reasonable to me. I would typically do an MDS plot over the first few dimensions to see what variables are important in a given data set. If there is good separation between samples based on any of these (tissue, genotype (hopefully yes to both!), flow cell, day of collection ( ...
written 13 days ago by Matthew Ritchie690
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Comment: C: How to extract the voom normalized value for each observation?
... The 'weights' output from running voomWithQualityWeights() already combines both the observational and sample-specific weights. These weights are relative though and only make sense in the context of a linear model (i.e. in a per gene analysis). I would not recommend just multiplying the logCPM va ...
written 10 weeks ago by Matthew Ritchie690
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Answer: A: voomWithQualityWeights: question on min. number of replicates per group + design
... Yes, this advice also applies when using voomWithQualityWeights on RNA-seq data. Using the actual design matrix will work best if you have 3 or more replicates per group with this model. If you have fewer than this, an intercept model is the best you can do. ...
written 12 weeks ago by Matthew Ritchie690
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News: BioCAsia, 17th November 2017, Adelaide, Australia
... The third Bioconductor Asia meeting (https://www.abacbs.org/conference-workshops#bioc2017-link) will be held on Friday 17th November 2017 in Adelaide, Australia as a satellite event to ABACBS 2017 (http://www.abacbs.org/conference/). This one-day event aims to bring together researchers with an int ...
news conference written 5 months ago by Matthew Ritchie690
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Answer: A: CRLMM: Error in quantile.default(M, c(1, 5)/6, names = FALSE)
... Apologies for the delay in replying. It's not the most helpful error message, but in my experience it is usually due to a mismatch between the annotation and chip type which introduces NAs into the intensity matrix for probes that are not present. If you send me a few idat files I can try and work ...
written 8 months ago by Matthew Ritchie690
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Answer: A: bug limma / illuminaio? Otherwise small feature request...
... Thanks for the suggestion Guido - will look into this. ...
written 9 months ago by Matthew Ritchie690
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Answer: A: Error with read.idat() function in illuminaio package
... I've made some changes in limma to accommodate idat files in SNP format. I'm not sure when this change will become publicly available though, so in the meantime, you can download an rda file containing data from this experiment read in using the commands below from http://bioinf.wehi.edu.au/folders/ ...
written 9 months ago by Matthew Ritchie690
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Answer: A: Using edgeR for small shRNA-seq screen analysis
... With a time-course design, the example in section 4 (see page 16 for the model) of the guide you refer to above is probably most relevant. In this example, the time-course was over 8 days and there were no replicates, so you will obviously need to adapt the design matrix to suit your experiment.  I ...
written 11 months ago by Matthew Ritchie690
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Answer: A: CRLMM: Which array type work with which annotation package
... Thanks for your question. For the HumanOmniExpress-24v1-1 and HumanOmniExpress-24v1-0 we don't have a package at this stage unfortunately. We are putting together a work around for cases like this, where the user specifies the annotation and sets  cdfName="nopackage" but I've just identified some b ...
written 16 months ago by Matthew Ritchie690
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Answer: A: Bug?: crlmm and cdfName not valid
... This error message means that the chip-specific package you need hasn't been installed. However, installing it in the usual way with biocLite() is currently impossible, because I haven't added it to Bioconductor! Try downloading from http://bioinf.wehi.edu.au/folders/mritchie/humanomniexpexome8v1p ...
written 16 months ago by Matthew Ritchie690

Latest awards to Matthew Ritchie

Scholar 2.5 years ago, created an answer that has been accepted. For A: Crlmm HumanOmniExpress-24v1 Annotation not available

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