User: Matt Settles

gravatar for Matt Settles
Matt Settles70
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11 years, 9 months ago
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Posts by Matt Settles

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Comment: C: affylmGUI segfault on "pd.ragene.1.0.st.v1"
... James, Wouldn't that depend on how the information is accessed? If affylmgui uses functions for ALL its data access from the cdf env, then I could create functions in oligo that return the requested information in the expected form regardless of the underlying data structure. If affylmgui accesses ...
written 10.4 years ago by Matt Settles70
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Comment: C: affylmGUI segfault on "pd.ragene.1.0.st.v1"
... Harry, Wolfgang and James, The exon and gene ST arrays do not use, or even have, a CDF file for the array, I think a requirement for makecdfenv. These arrays use clf and pgf files, hence the need for the oligo set of packages. You can try changing the name of pd.ragene.1.0.st.v to ragene10stv1cdf ...
written 10.4 years ago by Matt Settles70
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Continued problems with pdInfoBuilder (Matt Settles)
... Harry, I'm working with the devel version of pdInfoBuilder and am updating/adding components for building Gene ST pdInfo objects. Coincidently I'm building the pdInfo object for the Affy RaGene-1_0 array. I should have this complete in the next couple of days and can forward it on to you if you'd l ...
affy pdinfobuilder written 10.5 years ago by Matt Settles70
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Bioconductor Digest, Vol 68, Issue 7
... Dhiraj, Oligo, oligoClasses and pdInfoBuilder are undergoing some major upgrades for analysis of Nimblegen data (expression and tiling), they likely will not be available with this October release of Bioconductor but will be a part of the development version. In the meantime you can contact me dire ...
oligo pdinfobuilder oligoclasses written 10.6 years ago by Matt Settles70
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Answer: A: BSgenome package - add the bos taurus genome
... Herve and Joao, The most recent version of the bovine genome is 4.0 Oct 2007 ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/fasta/ It would however be helpful to have both 3.1 and 4.0 since many have not made the transition to the new assembly yet. Matt Settles Bioinformatics Core Washington State Univ ...
written 11.2 years ago by Matt Settles70
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Answer: A: Venn Diagram for 2, 3 and 4 sets (can be extended for
... Deal List, I had this problem a while back, so I had extended the limma vennDiagram function to work with 4 (not more) using the ellipse method some have eluded to. An example can be found http://bioinfo-mite.crb.wsu.edu/Rcode/pmaVenns.pdf and the code can be found http://bioinfo-mite.crb.wsu.edu ...
written 11.6 years ago by Matt Settles70
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simpleaffy QCstats and affyQAReport repost
... My apologizes for the previous unintelligible post, apparently Windows Live Mail does not allow for plain text emails. to whom are interested, I have two requests (with possible suggestions for updates). I use affyQAreport for every dataset and I really like the results. It is pretty complete and ...
zebrafish probe affy written 11.8 years ago by Matt Settles70 • updated 11.8 years ago by Crispin Miller1.1k

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