User: Matthew Ritchie

gravatar for Matthew Ritchie
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630
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Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Twitter:
mritchieau
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Google Scholar Page
Last seen:
1 week ago
Joined:
13 years, 3 months ago
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m*******@wehi.edu.au

Posts by Matthew Ritchie

<prev • 71 results • page 1 of 8 • next >
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Answer: A: bug limma / illuminaio? Otherwise small feature request...
... Thanks for the suggestion Guido - will look into this. ...
written 7 days ago by Matthew Ritchie630
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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 17 days ago by Matthew Ritchie630
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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 12 weeks ago by Matthew Ritchie630
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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 7 months ago by Matthew Ritchie630
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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 7 months ago by Matthew Ritchie630
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News: BioCAsia, 4th November 2016, Brisbane, Australia
... The second Bioconductor Asia-Pacific Developers' meeting will be held on 4th November 2016 in Brisbane, Australia as a satellite event to AB3CBS 2016 (http://www.abacbs.org/conference/). For more information, visit the meeting website http://www.abacbs.org/biocasia2016. If you'd like an opportunit ...
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Answer: A: Error in processAmplicons "hairpin sequence length not with specified length"
... This error message suggests you have hairpins of different lengths in your library. To check if this is the case, try running something like:  hp = read.delim("Hairpins sense.txt", stringsAsFactors=FALSE) dim(hp) summary(sapply(hp$Seq, FUN="nchar")) which(sapply(hp$Seq, FUN="nchar")!=22) hp[sappl ...
written 12 months ago by Matthew Ritchie630
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Comment: C: edgeR:processAmplicons barcode match only 57% when it should be 100% -- I artifi
... Sounds like a bug with your code rather than ours! This function assumes sequence reads are in fastq format - if this is messed up you might find strange results. ...
written 17 months ago by Matthew Ritchie630
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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 19 months ago by Matthew Ritchie630
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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 19 months ago by Matthew Ritchie630

Latest awards to Matthew Ritchie

Scholar 21 months ago, created an answer that has been accepted. For A: Crlmm HumanOmniExpress-24v1 Annotation not available

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