User: Matthew Ritchie

gravatar for Matthew Ritchie
Reputation:
660
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Twitter:
mritchieau
Scholar ID:
Google Scholar Page
Last seen:
2 months, 2 weeks ago
Joined:
13 years, 9 months ago
Email:
m*******@wehi.edu.au

Posts by Matthew Ritchie

<prev • 73 results • page 1 of 8 • next >
3
votes
0
answers
508
views
0
answers
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 11 weeks ago by Matthew Ritchie660
0
votes
1
answers
307
views
1
answers
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 5 months ago by Matthew Ritchie660
0
votes
1
answers
165
views
1
answers
Answer: A: bug limma / illuminaio? Otherwise small feature request...
... Thanks for the suggestion Guido - will look into this. ...
written 6 months ago by Matthew Ritchie660
0
votes
3
answers
629
views
3
answers
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 6 months ago by Matthew Ritchie660
0
votes
2
answers
249
views
2
answers
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 8 months ago by Matthew Ritchie660
0
votes
1
answers
299
views
1
answers
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 13 months ago by Matthew Ritchie660
0
votes
1
answers
226
views
1
answers
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 13 months ago by Matthew Ritchie660
1
vote
0
answers
406
views
0
answers
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 ...
0
votes
1
answers
256
views
1
answers
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 18 months ago by Matthew Ritchie660
0
votes
2
answers
439
views
2
answers
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 23 months ago by Matthew Ritchie660

Latest awards to Matthew Ritchie

Scholar 2.3 years ago, created an answer that has been accepted. For A: Crlmm HumanOmniExpress-24v1 Annotation not available

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 151 users visited in the last hour