User: Matthew Ritchie

gravatar for Matthew Ritchie
Reputation:
750
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Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Twitter:
mritchieau
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Google Scholar Page
Last seen:
2 weeks, 1 day ago
Joined:
15 years, 4 months ago
Email:
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Posts by Matthew Ritchie

<prev • 79 results • page 1 of 8 • next >
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Answer: A: voomWithQualityWeights together with covariate in design matrix
... If the MDS / PCA plot from your experiment shows systematic separation of samples based on cell number (e.g. PC1 or PC2 shows a gradient of samples with high cell number on one side of the plot through to low cell number on the other side - try colour coding samples by cell number to make this easie ...
written 19 days ago by Matthew Ritchie750
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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 11 months ago by Matthew Ritchie750
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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 16 months ago by Matthew Ritchie750
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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 16 months ago by Matthew Ritchie750
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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 18 months ago by Matthew Ritchie750
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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 19 months ago by Matthew Ritchie750
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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 22 months ago by Matthew Ritchie750
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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 2.1 years ago by Matthew Ritchie750
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Answer: A: bug limma / illuminaio? Otherwise small feature request...
... Thanks for the suggestion Guido - will look into this. ...
written 2.1 years ago by Matthew Ritchie750
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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 2.1 years ago by Matthew Ritchie750

Latest awards to Matthew Ritchie

Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: voomWithQualityWeights: question on min. number of replicates per group + design
Scholar 3.9 years ago, created an answer that has been accepted. For A: Crlmm HumanOmniExpress-24v1 Annotation not available

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