User: Matthew Ritchie

gravatar for Matthew Ritchie
Reputation:
730
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Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Twitter:
mritchieau
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Google Scholar Page
Last seen:
3 months, 2 weeks ago
Joined:
14 years, 9 months ago
Email:
m*******@wehi.edu.au

Posts by Matthew Ritchie

<prev • 78 results • page 1 of 8 • next >
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Comment: C: ProcessAmplicons using very little memory on big job?
... This function breaks the data into smaller chunks that it processes serially, so you shouldn't need 30G of memory. It also shouldn't take that long to process the first 10 million reads. Can you provide the example code and sessionInfo() and a small sample of the sequences from your FASTQ file (perh ...
written 4 months ago by Matthew Ritchie730
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News: Bioconductor at useR! 2018
... Dear Bioconductors, At useR! 2018 (https://user2018.r-project.org/) we are planning a special Bioconductor session. If you are considering a trip to Brisbane (Australia) this July (10th-13th) be sure to submit an abstract to highlight your great work to fellow R/Bioconductor enthusiasts. Abstract ...
news R bioconductor conference written 9 months ago by Matthew Ritchie730
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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 10 months ago by Matthew Ritchie730
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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 12 months ago by Matthew Ritchie730
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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 months ago by Matthew Ritchie730
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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 15 months ago by Matthew Ritchie730
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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 18 months ago by Matthew Ritchie730
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Answer: A: bug limma / illuminaio? Otherwise small feature request...
... Thanks for the suggestion Guido - will look into this. ...
written 19 months ago by Matthew Ritchie730
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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 19 months ago by Matthew Ritchie730
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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 21 months ago by Matthew Ritchie730

Latest awards to Matthew Ritchie

Teacher 18 months ago, created an answer with at least 3 up-votes. For A: voomWithQualityWeights: question on min. number of replicates per group + design
Scholar 3.4 years ago, created an answer that has been accepted. For A: Crlmm HumanOmniExpress-24v1 Annotation not available

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