User: Steven McKinney

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Posts by Steven McKinney

<prev • 31 results • page 1 of 4 • next >
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Affymetrix HTA 2 array analysis
... Hi all, Has anyone developed bioconductor/R analysis tools for the Affymetrix Human Transcriptome Array HTA_2_0 ? Any information on processing data from this chip type would be appreciated. Best Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer ...
cancer breast written 4.6 years ago by Steven McKinney310
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Comment: C: Mapping chromosome and nucleotide position to gene name
... Thanks Steve, The thread ideas work beautifully. Thanks also to Martin Morgan for his ideas. Best Steve McKinney > -----Original Message----- > From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] > Sent: Thursday, April 16, 2009 1:03 PM > To: Steven McKinney > Cc ...
written 8.6 years ago by Steven McKinney310
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Mapping chromosome and nucleotide position to gene name
... Hi all, >From the output of a custom HMM routine, I have data showing chromosome number and nucleotide position, but no associated gene name or database identifier. e.g. > logRiList[[1]][1:10,] chromosome position end logR state 1 1 10004 10004 0.7627 3 2 ...
cancer breast written 8.6 years ago by Steven McKinney310 • updated 8.6 years ago by Steve Lianoglou12k
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Loading problem with Rlibstree and microRNA packages on MacOS X 10.4
... Hi Duncan, I thought Rlibstree might not be maintained as the README states "This is a quickly written interface... ", has no vignette or pdf, and references an older version of libstree "libstree-0.4.0.tar.gz" so it wasn't clear when this package was last touched. My apologies for that judgment. ...
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Loading problem with Rlibstree and microRNA packages on MacOS X 10.4
... Dear Luo, The README file in the Rlibstree source directory discusses installing the software 'libstree'. I downloaded libstree from http://www.icir.org/christian/libstree/ and attempted to configure and make, but libstree would not make. bash-3.2$ make make all-recursive Making all in src if /b ...
cancer breast rtracklayer microrna written 9.0 years ago by Steven McKinney310 • updated 9.0 years ago by Luo Weijun1.4k
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Comment: C: Creating a new instance of oligoSnpSet
... Hi Martin, Thanks for your feedback. I've put requested info inline below. I'll work on a reproduce with manageable data. Best Steve McKinney > -----Original Message----- > From: Martin Morgan [mailto:mtmorgan at fhcrc.org] > Sent: Wednesday, November 26, 2008 1:23 PM > To: Steven ...
written 9.0 years ago by Steven McKinney310
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Answer: A: Creating a new instance of oligoSnpSet
... Hi all, Thanks to Robert Scharpf for a quick and detailed off-line response. For anyone else that may encounter this issue: my problem was that my featureData object's 'data' slot data frame did not have names "chromosome" and "position" . I originally defined my featureData object as > cclf ...
written 9.0 years ago by Steven McKinney310
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Creating a new instance of oligoSnpSet
... Hello All, I am trying to get some Illumina HumanCNV370-Quad data into VanillaICE to do some copy number analysis. In attempting to create an object of class "oligoSnpSet" I can not seem to specify an annotation that works. e.g. as specified in a vignette > cclss <- + new("oligoSnpSet", ...
annotation cancer breast vanillaice copynumber written 9.0 years ago by Steven McKinney310
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Answer: A: Processing data from Illumina HumanCNV370-Quad chips
... Hi Jan, Thanks very much for these guidelines. Getting the annotations into the final report via BeadStudio, plus the sample sheet, yielded a successful pair of files to get the data read in. > ccld <- read.SnpSetIllumina(samplesheet = "ccl_CNV370SampleSheet_8samples.csv", + ...
written 9.0 years ago by Steven McKinney310
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Processing data from Illumina HumanCNV370-Quad chips
... Hi all, Has anyone processed data from Illumina HumanCNV370-Quad chips using Bioconductor or other open source software? I've started attempts to read data using beadarraySNP but have not had luck yet. > SNPdata <- read.SnpSetIllumina("Gulisa_CNV370SampleSheet_8samples.csv") Error in read.S ...
cancer breast written 9.0 years ago by Steven McKinney310

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