User: Alicia Oshlack

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Posts by Alicia Oshlack

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Comment: C: RNASeq: normalization issues
... Hi Joao, I must say we are in the early stages of dealing with this issue so I'm reluctant to give advice on an issue that we haven't fully explored yet. So far we really only observe this issue in very large datasets. When I have some firmer results I'll let you know. Sorry I can't be more help. ...
written 8.5 years ago by Alicia Oshlack70
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Answer: A: RNASeq: normalization issues
... > Send Bioconductor mailing list submissions to > bioconductor at r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/bioconductor > or, via email, send a message with subject or body 'help' to > b ...
written 8.5 years ago by Alicia Oshlack70
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Bioinformatics Post-doc in Melbourne
... The Bioinformatics group at the Murdoch Childrens Research Institute, in Melbourne, Australia is a newly established and rapidly expanding research group. We have an exciting opportunity for post-doctoral research fellow to join the Oshlack group. The new appointee will be working on high-throughput ...
sequencing written 8.5 years ago by Alicia Oshlack70
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Subject: Re: Normalization of arrays where most of the genes change
... Hi Yiwen, In cases where you know the subset of genes that are not changin you can use limma as outlined in: http://genomebiology.com/2007/8/1/R2 Cheers, Alicia Message-ID: Sean, Thanks for getting back to me so quickly! I took a look at the VSN package and some threads in the mailing ...
normalization vsn limma written 10.4 years ago by Alicia Oshlack70
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Detecting mRNA Expression When Somatic Mutations Have
... > > Message: 10 > Date: Fri, 5 Dec 2008 15:40:16 -0700 > From: "Stephen Piccolo" > Subject: [BioC] Detecting mRNA Expression When Somatic Mutations Have > Occurred > To: > Message-ID: <4939adcf.1e068e0a.67c0.ffffd8d7 at mx.google.com> > Content-Type: text/pl ...
microarray cancer written 10.9 years ago by Alicia Oshlack70
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Answer: A: cross species CGH Nimblegene arrays
... Hi, I think they did chimp on a human array in this paper: http://www.pnas.org/cgi/content/full/103/21/8006 Also, we published some cross-species microarray mRNA work in this paper and so if you are doing within species comparisons your idea should work to the extent that you can map the probes: ...
written 11.4 years ago by Alicia Oshlack70
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Answer: A: OT: Problems with Nimblegen scans?
... Hi Jose, We experienced a similar thing with our custom Nimblegen arrays. We asked them to rescan the arrays again at a lower setting which improved things a bit but we still had some saturated probes. Cheers, Alicia Alicia Oshlack, PhD Division of Bioinformatics Walter and Eliza Hall Institute ...
written 12.3 years ago by Alicia Oshlack70

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