User: Ken Simpson

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Ken Simpson70
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13 years, 7 months ago
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16 years, 1 month ago
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k*******@wehi.edu.au

Posts by Ken Simpson

<prev • 7 results • page 1 of 1 • next >
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Answer: A: error in mas5calls() for soybean chip
... Hi Jenny, > > PMAcalls <- mas5calls(rawdata[,1:5]) > Getting probe level data... > Computing p-values > Making P/M/A Calls > Error in if (y < alpha1) { : missing value where TRUE/FALSE needed > > > PMAcalls <- mas5calls(rawdata[,1:5],alpha1=0.04,alpha2=0.06) & ...
written 13.6 years ago by Ken Simpson70
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RNA degradation... or not?
... Dear Bioconductors, I apologise if this is not 100% appropriate for the list. I have seen data sets from a couple of experiments lately, each using four MOE430 version 2 chips, in which one chip of the four has a median PM which is a factor of three or four higher than on the others. When I do a ...
genetics written 14.8 years ago by Ken Simpson70 • updated 14.8 years ago by James W. MacDonald52k
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Custom CDF files
... Rich, Unless I am mistaken, it doesn't sound like you have made a CDF environment for your custom probe sets yet. You will have to do that first. You need to use makecdfenv to create a package containing the environment, then install the package. Supposing your CDF package is called newcdf, yo ...
chipname cdf probe makecdfenv gcrma written 14.9 years ago by Ken Simpson70
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Answer: A: limma and spottypes
... Hi Simon, Looks like that part of the user guide is out of date. controlStatus() should do what you want. (do help.start(), then click on Packages and then limma, and consult section 3: ReadingData) Cheers, Ken On Sun, 21 Dec 2003, Simon Melov wrote: > Hi, > I'm trying to plot some spot ...
written 16.0 years ago by Ken Simpson70
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Answer: A: Bioconductor Problem
... > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: > Specified environment specified did not contain RAE230A > Library - package rae230acdf not installed > Data for package affy did not contain RAE230A > Bioconductor - rae230acdf not availab ...
written 16.0 years ago by Ken Simpson70
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Answer: A: Annotating yeast ORFs with GO and KEGG
... Hi Shih-Te, Use the lookUp function (devel version of the annotate package) or multiget (older version) to obtain the quantities of interest. e.g. > lookUp("YAL001C","YEAST","GO") "GO:0000127" "GO:0003709" "GO:0006384" > multiget(c("YAL001C","YAL002W"),envir=YEA ...
written 16.1 years ago by Ken Simpson70
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Answer: A: add gcrma to bgcorrect methods in rma
... Hi Anthony, You should just be able to do library(gcrma) bgcorrect.methods <- c(bgcorrect.methods, "gcrma") Cheers, Ken On Thu, 6 Nov 2003, Anthony Bosco wrote: > Hi. > > How do I add gcrma as a background subtraction method so I can use it > in expresso function. > > > ...
written 16.1 years ago by Ken Simpson70

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