User: Ben Bolstad

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Ben Bolstad1.2k
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Posts by Ben Bolstad

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Answer: A: affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
... Hi Jim, Grabbing some data from GEO and testing, as far as I can tell the current affy 1.33.2 image() command is fine for HuGene 1.1 st, at least if you use the brainarray cdfenv. Similarly the affyPLM images look correctly oriented etc. One note, ncol() and nrow() on an AffyBatch object do look ...
written 7.5 years ago by Ben Bolstad1.2k
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Comment: C: affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
... I probably should not be responding, lest I say something stupid (though I agree that I am highly imperfect). Plus, I am away from both my email archives and any sort of machine that I can use to test things out which only exacerbates the chances of incorrectness. However, any changes that I made w ...
written 7.5 years ago by Ben Bolstad1.2k
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Answer: A: preprocessCore "Undefined log2" installation error
... I believe I may have already addressed this in the development branch (meaning it will be fixed in the next BioC release), but please do confirm for me the version of preprocessCore that you are using. Best, Ben > I'm running FreeBSD8.2 on an Intel Core2Duo > I have installed the basic R p ...
written 8.3 years ago by Ben Bolstad1.2k
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Answer: A: GCRMA: feature request
... At least in theory you should be able to accomplish this also via affyPLM's threestep() function, though I have not tested against any modifications that might have occured to GCRMA in the last 3-4 years. eg eset <- threestep(abatch,background.method="GCRMA",normalize.method="quantile" ,summary ...
written 8.5 years ago by Ben Bolstad1.2k
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Comment: C: Can not install 'affyio' with compiler icc on redhat linux ES5
... icc has not previously been supported. I am planning to investigate how to improve the codes portability. Ben -----Original Message----- From: Dan Tenenbaum Sent: Monday, November 29, 2010 10:42 AM To: Zhenguo Zhang ; Ben Bolstad Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Can not in ...
written 8.6 years ago by Ben Bolstad1.2k
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Answer: A: identical output plots for NUSE AND RLE
... You might want to try using the NUSE() and RLE() functions directly rather than the boxplot method. Best, Ben -------------------------------------------------- From: "Richard Friedman" Sent: Tuesday, June 22, 2010 6:32 AM To: "bio c bioconductor" Subject: [BioC] identical output plots for NUSE ...
written 9.1 years ago by Ben Bolstad1.2k
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Problems in MAplot for affybatch objects
... It has been fixed in affy 1.26.1/1.27.1 (Release/Devel) which will show up in the builds sometime in the next few days. Ben On Wed, 2010-04-28 at 10:49 +0200, Javier P?rez Florido wrote: > Dear Ben, > I've installed the new version of both R and affyPLM package (1.24), but > the problem ...
affy affyplm written 9.2 years ago by Ben Bolstad1.2k
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Answer: A: Question about quantile normalization in normalize.AffyBatch.quantiles
... Almost certainly what you are seeing is a reflection of the fact that the quantile normalization code underlying normalize.AffyBatch.quantiles is designed to handle ties. Basically, the algorithm attempts to ensure that data values that are exactly equal on input within a specific array (column) are ...
written 9.2 years ago by Ben Bolstad1.2k
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Answer: A: an error in normalize.quantiles {preprocessCore} function?
... Without actually looking at your data, a reasonable explanation for what you have observed would be in the handling of ties. The algorithm ensures that values that are equal on input in a given column are also equal on output. > set.seed(1) > X <- rnorm(100000) > X <- round(X,3) ### ...
written 9.3 years ago by Ben Bolstad1.2k
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Answer: A: Problems in MAplot for affybatch objects
... Hi Javier, You have indeed found discrepant behavior that should be fixed. MAplot for ExpressionSet object is implemented in affyPLM, MAplot for AffyBatch objects is implemented in affy. So it is not really the same set of code being executed in each case. But the basic behavior was intended to be ...
written 9.3 years ago by Ben Bolstad1.2k

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