User: Matthew Ritchie

gravatar for Matthew Ritchie
Reputation:
750
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Twitter:
mritchieau
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Google Scholar Page
Last seen:
3 months, 1 week ago
Joined:
15 years, 6 months ago
Email:
m*******@wehi.edu.au

Posts by Matthew Ritchie

<prev • 79 results • page 2 of 8 • next >
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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 2.5 years ago by Matthew Ritchie750
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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 2.9 years ago by Matthew Ritchie750
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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 2.9 years ago by Matthew Ritchie750
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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 3.4 years ago by Matthew Ritchie750
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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 3.8 years ago by Matthew Ritchie750
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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 3.9 years ago by Matthew Ritchie750
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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 3.9 years ago by Matthew Ritchie750
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Answer: A: crlmm crossprod error, and missing files in annotation
... Hmm - not sure then. If you can provide a few examples IDAT files offline, I will take a closer look. ...
written 4.1 years ago by Matthew Ritchie750
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Answer: A: crlmm crossprod error, and missing files in annotation
... Are these OmniExpress24v1 chips referred to in your previous post? The OmniExpress12v1b package you're using above probably won't work for this platform as the probe IDs are likely to be different. We need to add a more informative error message here, but it generally arises when a chip type mismatc ...
written 4.1 years ago by Matthew Ritchie750

Latest awards to Matthew Ritchie

Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: voomWithQualityWeights: question on min. number of replicates per group + design
Scholar 4.1 years ago, created an answer that has been accepted. For A: Crlmm HumanOmniExpress-24v1 Annotation not available

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