## User: Matthew Ritchie

Reputation:
730
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
mritchieau
Scholar ID:
Last seen:
3 months, 3 weeks ago
Joined:
14 years, 3 months ago
Email:
m*******@wehi.edu.au

#### Posts by Matthew Ritchie

<prev • 77 results • page 2 of 8 • next >
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... 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 20 months ago by Matthew Ritchie730
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... 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 ...
written 23 months ago by Matthew Ritchie730
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... 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 2.1 years ago by Matthew Ritchie730
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... 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 2.5 years ago by Matthew Ritchie730
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... 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 2.6 years ago by Matthew Ritchie730
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... 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 2.7 years ago by Matthew Ritchie730
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... Hmm - not sure then. If you can provide a few examples IDAT files offline, I will take a closer look. ...
written 2.9 years ago by Matthew Ritchie730
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... 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 2.9 years ago by Matthew Ritchie730
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... Hi Andrew, We don't currently support this platform, but are working towards an approach to handle data from any arbitrary platform without the need for a chip-specific package - we hope to make it available in the next release. Best wishes, Matt ...
written 2.9 years ago by Matthew Ritchie730
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... Thanks for providing the example files. The problem was caused by a single probe that was listed in the manifest file but wasn't in the idat file. Have added a new 'tolerance' argument to read.idat in the devel version of limma (v 3.25.13, should be available over the next few days) to handle this. ...
written 3.0 years ago by Matthew Ritchie730

#### Latest awards to Matthew Ritchie

Teacher 12 months ago, created an answer with at least 3 up-votes. For A: voomWithQualityWeights: question on min. number of replicates per group + design
Scholar 2.9 years ago, created an answer that has been accepted. For A: Crlmm HumanOmniExpress-24v1 Annotation not available

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