User: Paul Boutros

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Paul Boutros330
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Posts by Paul Boutros

<prev • 33 results • page 1 of 4 • next >
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minor fitPLM bug in get.psi.code
... Hello, I think there's a minor bug in get.psi.code of fitPLM. Here's the function: > get.psi.code function (name) { psi.names <- c("Huber", "fair", "Cauchy", "Geman-McClure", "Welsch", "Tukey", "Andrews") if (!is.element(name, psi.names)) { stop(paste(name, "is not a ...
written 10.8 years ago by Paul Boutros330
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Answer: A: Loading multiple Affy chips simultaneously
... I just realized I forgot to give some basic information on my system: R 2.4.1 affy 1.12.2 gcrma 2.6.0 Windows XP Paul -----Original Message----- From: Paul Boutros [mailto:Paul.Boutros@utoronto.ca] Sent: Saturday, January 27, 2007 1:59 PM To: 'bioconductor at stat.math.ethz.ch' Subject: Loading mu ...
written 12.3 years ago by Paul Boutros330
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Loading multiple Affy chips simultaneously
... Hello, I'm trying to analyze & merge some rat data that was generated on two separate Affymetrix chips (RAE230-A and RAE230-2). One chip (RAE230-2) is a superset of the other. Approximately equal numbers of animals were analyzed with the smaller array (n=9) as the larger (n=10). I would like ...
go cdf gcrma written 12.3 years ago by Paul Boutros330
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Comment: C: siggenes permutation count problem
... Hi Jim (and others who replied off-list), Thank you -- when I saw the term "complete permutations", it didn't register in my head that it really meant combinations. Paul Quoting "James W. MacDonald" : > paul.boutros at utoronto.ca wrote: > > Hello, > > > > I'm having some tr ...
written 13.4 years ago by Paul Boutros330
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siggenes permutation count problem
... Hello, I'm having some troubles interpreting how/why siggenes performed a certain number of permutations on my dataset. This is an affy dataset that was normalized by: data <- ReadAffy(filenames=cel.files, phenoData="phenodata.txt"); eset <- expresso(data, normalize.method="constant", bgcor ...
normalization affy siggenes written 13.4 years ago by Paul Boutros330 • updated 13.4 years ago by James W. MacDonald50k
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Error setting boxplot title in Affy
... Hi again, I've been some troubles setting the title for boxplots of AffyBatch objects. The output is below. I was hoping to suggest a patch but... I actually couldn't find the source anywhere in my win32 distribution -- only a compiled DLL and RDA files. I'm using R 2.0.0 and Affy 1.5.8 on window ...
affy written 14.4 years ago by Paul Boutros330 • updated 14.4 years ago by James W. MacDonald50k
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Answer: A: logical subscript too long in normalizeRobustSpline
... For anybody who replicates this error: Gordon was right -- I had the array layout mis-set. When using debug, I uncovered a webset on debugging suggestions for R that was pretty helpful: http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/ Paul > -----Original Message----- > From: Go ...
written 14.5 years ago by Paul Boutros330
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logical subscript too long in normalizeRobustSpline
... Hi again, Getting this error using robustspline normalization in limma: Error in normalizeRobustSpline(object$M[, j], object$A[, j], layout, df = df, : (subscript) logical subscript too long I'm on: Win2k SP2 R 2.0 limma 1.8.8 This isn't a general problem with robustspline, as I seem to ...
normalization written 14.6 years ago by Paul Boutros330
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Minor Bug in limma 1.8.8 changeLog()
... WinXP R 2.0.0 limma 1.8.8 changeLog appears to not accept arguments anymore: function (n = 20) { writeLines(readLines(system.file("doc/changelog.txt", package = "limma"), n = 20)) } Paul ...
written 14.6 years ago by Paul Boutros330 • updated 14.6 years ago by Gordon Smyth37k
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(no subject)
... >Date: Thu, 9 Sep 2004 22:01:22 +1000 (EST) >From: "Gordon K Smyth" >Subject: Re: [BioC] Finding and controlling for dye bias in Limma >To: "Sean Davis" >Cc: Bioconductor > >> We have several samples hybed on two-color arrays (treated versus >> untreated). Half are ...
limma written 14.7 years ago by Paul Boutros330

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Popular Question 10.8 years ago, created a question with more than 1,000 views. For Increasing rlm iterations for convergence in limma's normalizeRobustSpline

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