User: Dick Beyer
Dick Beyer • 1.4k
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Posts by Dick Beyer
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... 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
**************************** ...
written 6.7 years ago by
Dick Beyer • 1.4k
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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 6.8 years ago by
Dick Beyer • 1.4k
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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 6.8 years ago by
Dick Beyer • 1.4k
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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 6.8 years ago by
Dick Beyer • 1.4k
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... 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 6.8 years ago by
Dick Beyer • 1.4k
• updated
6.8 years ago by
Dan Tenenbaum • 8.2k
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... 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 ...
written 7.9 years ago by
Dick Beyer • 1.4k
• updated
7.9 years ago by
Mike Smith • 3.8k
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... 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
...
written 8.1 years ago by
Dick Beyer • 1.4k
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... 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") ...
written 8.1 years ago by
Dick Beyer • 1.4k
0
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... 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 ...
written 8.2 years ago by
Dick Beyer • 1.4k
• updated
8.2 years ago by
Wolfgang Huber ♦ 13k
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... 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 8.4 years ago by
Dick Beyer • 1.4k
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