User: Dick Beyer

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Dick Beyer1.4k
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Posts by Dick Beyer

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Bioconductor Digest, Vol 117, Issue 6
... Hi Sainitin, I'd guess your problem is your "s"i matrix. I say that because of your line of code: si.gnames<-si[,1] If you are send "si" to RPadvance, then RPadvance doesn't know what to do with the first column, as it thinks that should be numerical. Cheers, Dick **************************** ...
affy written 5.1 years ago by Dick Beyer1.4k
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Comment: C: getBM weird error
... Thanks Dan and Steffen and Jim, All is well now. Sorry to bother everyone due to not completely updating my installation. Thanks much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env ...
written 5.1 years ago by Dick Beyer1.4k
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Comment: C: getBM weird error
... Hi Jim, Sorry, I forgot my sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC ...
written 5.1 years ago by Dick Beyer1.4k
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Comment: C: getBM weird error
... Hi Jim, I tried that, but got this: mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", host="www.ensembl.org") Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Error: 1: Space required after the Public Identifier 2: Sy ...
written 5.1 years ago by Dick Beyer1.4k
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getBM weird error
... I'm hoping someone might have a work-around for this getBM problem: library(biomaRt) mart <- useMart( "ensembl", dataset="mmusculus_gene_ensembl") tmp <- getBM(attributes=c("uniprot_swissprot_accession","ipi"), filters="ipi", values="IPI00134704", mart=mart) Error in getBM(attributes = c("un ...
written 5.1 years ago by Dick Beyer1.4k • updated 5.1 years ago by Dan Tenenbaum ♦♦ 8.2k
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lumi and/or beadarray for getting beadSummary
... I'm hoping someone can point me in the right direction. Some months ago I analyzed some Illumina mouse data using the lumi() package since the data received was a beadSummary data file. As I sort of understand things, this is a summary file output by Illumina's GenomicStudio software (or maybe it ...
microarray annotation ebimage written 6.2 years ago by Dick Beyer1.4k • updated 6.2 years ago by Mike Smith2.1k
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Biostats/Bioinformatics job University of Washington
... I'd like to bring a job announcement to people's attention: https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szCate gory=jobprofile&szOrderID=74551&szCandidateID=0&szSearchWords=&szRetur nToSearch=1 This is a position doing microarray and other OMICs analysis in our ...
microarray written 6.4 years ago by Dick Beyer1.4k
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pdmClass plot error
... Hi Jim, I am using the pdmclass package and had a question. I'd like to be able to plot the output from pdmClass when there are only 2 levels. However, that generates an error. Here is the example from the pdf documentation with a change to show the problem: library("pdmclass") data("fibroEset") ...
pdmclass written 6.4 years ago by Dick Beyer1.4k
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Problem with BGandNorm() from the Agi4x44PreProcess package
... Hello, I've run into a problem that looks like the function BGandNorm() is broken because it relies on vsn as a method called by normalizeBetweenArrays, but that method has been replaced by a function normalizeVSN(). Here is some output that shows the problem: > dd <- read.AgilentFE(targets ...
vsn written 6.6 years ago by Dick Beyer1.4k • updated 6.6 years ago by Wolfgang Huber13k
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Answer: A: DEGraph demo exprData question
... Hi Pierre, Perfect! Thanks very much for your thorough explanation. Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 ...
written 6.7 years ago by Dick Beyer1.4k

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Centurion 5.1 years ago, created 100 posts.

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