User: Matthew Ritchie

gravatar for Matthew Ritchie
Reputation:
780
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Location:
Australia
Website:
http://www.wehi.edu.au...
Twitter:
mritchieau
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Google Scholar Page
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2 weeks, 1 day ago
Joined:
15 years, 8 months ago
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Posts by Matthew Ritchie

<prev • 80 results • page 1 of 8 • next >
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News: Bioconductor Community Survey
... Dear Bioconductors, On behalf of Bioconductor's [Technical Advisory Board][1], the first community survey has been launched to collect feedback on the project and help guide future activities. Please take a few minutes to complete the survey, which is available from [here][2]. Thanks in advance ...
news feedback community written 16 days ago by Matthew Ritchie780
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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 4 months ago by Matthew Ritchie780
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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 15 months ago by Matthew Ritchie780
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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 20 months ago by Matthew Ritchie780
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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 20 months ago by Matthew Ritchie780
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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 22 months ago by Matthew Ritchie780
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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 23 months ago by Matthew Ritchie780
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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 2.1 years ago by Matthew Ritchie780
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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 2.4 years ago by Matthew Ritchie780
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Answer: A: bug limma / illuminaio? Otherwise small feature request...
... Thanks for the suggestion Guido - will look into this. ...
written 2.4 years ago by Matthew Ritchie780

Latest awards to Matthew Ritchie

Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: voomWithQualityWeights: question on min. number of replicates per group + design
Scholar 4.2 years ago, created an answer that has been accepted. For A: Crlmm HumanOmniExpress-24v1 Annotation not available

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