User: John Coulthard

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Posts by John Coulthard

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biomaRt 'Please report this to the mailing list'
... Hi When following the instructions in the biomaRt.pdf I get the error below which ends 'Please report this to the mailing list'. Did I do something wrong or do I wait for something to be fixed? I am behind a proxy server but I can download packages so I don't think that is the issue. Many thanks ...
process biomart written 7.3 years ago by John Coulthard170 • updated 7.3 years ago by Sean Davis21k
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Comment: C: Rsamtools installation
... Thanks, this seems to have solved the issue for me. Your help is much appreciated. John Date: Thu, 10 Nov 2011 09:34:42 -0500 Subject: Re: [BioC] Rsamtools installation From: stvjc@channing.harvard.edu To: bahhab@hotmail.com CC: bioconductor@r-project.org; jmacdon@med.umich.edu on second thought ...
written 8.0 years ago by John Coulthard170
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Comment: C: Rsamtools installation
... Hi I purged R from the system and installed a fresh. Then opened R, issued these commands and got the same error as before... > source("http://www.bioconductor.org/biocLite.R") > biocLite("ArrayExpressHTS") > biocLite("ShortRead") > biocLite("Rsamtools") ** preparing package for laz ...
written 8.0 years ago by John Coulthard170
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Rsamtools installation
... Hi I'm trying to install Rsamtools and getting errors! I've tried... install.packages("/home/ann/downloads/Rsamtools_1.6.0.tar.gz") and biocLite("Rsamtools") (see below) Why doesn't biocLite() install the current version? I'm almost sure the dependencies are all up-to-date using inst ...
rsamtools written 8.0 years ago by John Coulthard170 • updated 8.0 years ago by James W. MacDonald51k
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Comment: C: removeBatchEffect problem
... > Date: Thu, 20 Oct 2011 11:32:30 -0400 > From: jmacdon@med.umich.edu > To: bahhab@hotmail.com > CC: bioconductor@r-project.org > Subject: Re: [BioC] removeBatchEffect problem > > Hi John, > > I don't know what to tell you. > > > x > [,1] [,2] ...
written 8.1 years ago by John Coulthard170
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Comment: C: removeBatchEffect problem
... Thanks Jim, but still regardless of the design matrix I give it the output is the same?! I must be missing something else. > design <- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8) )) > head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2),desig n=design)[,1:6]) ...
written 8.1 years ago by John Coulthard170
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removeBatchEffect problem
... Hi I'm having troubles with the removeBatchEffect function. It seems that whatever I put in as the 'design' I get the same result out of removeBatchEffect(); Perhaps I'm not using the right syntax for the 'design'? Below is each line of the function run individually and the output from the line ...
written 8.1 years ago by John Coulthard170 • updated 8.1 years ago by James W. MacDonald51k
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readQpcrBatch()
... Dear list Using the qpcrNorm package I can read single data files into R with readQpcr() but when I try to read in multiple files with readQpcrBatch() I'm getting an error and I don't understand what it's trying to tell me. Please see below. Many thanks John [john@y90-w-d RAT]$ R --vanilla R v ...
qpcrnorm written 8.5 years ago by John Coulthard170 • updated 8.5 years ago by Valerie Obenchain6.7k
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Comment: C: xps and unifilter; Error: UnitID not found; error in function ‘ExportData’
... Dear Christian That is working great now, thank you. One last thing. validData() is reporting the same value for P-Value and P-Adjusted. Was I supposed to set a flag somewhere to say what kind of adjusted P.value I wanted, if so where? The P-value I'm getting is un-adjusted, yes? Thanks for you ...
written 9.4 years ago by John Coulthard170
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Comment: C: xps and unifilter; Error: UnitID not found; error in function ‘ExportData’
... Dear Christian Yes. Exactly what I did was... > library(xps) > scheme.HuEx.1.0.st.v2<-import.exon.scheme(filename = "HuEx- 1_0-st-v2", layoutfile = "HuEx-1_0-st-v2.r2.clf", schemefile ="HuEx- 1_0-st-v2.r2.pgf", probeset="HuEx-1_0-st-v2.na30.hg19.probeset.csv", transcript ="HuEx-1_0-st ...
written 9.4 years ago by John Coulthard170

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