User: Michael Benjamin

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Posts by Michael Benjamin

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Comment: C: High-performance Bioconductor experiments
... This is the most exciting, and cryptic, part of the message... > which you can then normalize and scale. The normalizing and scaling > can, of course also be split up across processors. How? I was able to use snow to split up the CEL file readings--it's actually not that hard. cl<-makeC ...
written 16.0 years ago by Michael Benjamin120
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Comment: C: limma package
... Progress update (summarized from my forum for such matters at http://www.theschedule.net/forum/gforum.cgi?forum=20&do=forum_view): Briefly, I created a four-node cluster out of Pentium-III boxes and Debian Linux/openMosix. I saw no significant performance boost of ReadAffy or expresso using th ...
written 16.0 years ago by Michael Benjamin120
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Answer: A: (no subject)
... Thoughts: XML installation is tough. Try manually downloading the package source .gz for as many versions as you can find, then install that. Try installing the R XML package (not just the Bioconductor XML package). Only the "devel" version of AnnBuilder, I think 1.3.5, installed for me. Good l ...
written 16.0 years ago by Michael Benjamin120
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Comment: C: Annotation Questions
... Inspired by Ramon Diaz-Uriarte, I wanted to see how R/Bioconductor works on a cluster. After a few false starts, I successfully linked three lab computers (my laptop, a P-III 750 and a P-4 1.7) using openMosix. I found an easy solution in Cluster Knoppix, which magically turns Win- 2k boxes into c ...
written 16.0 years ago by Michael Benjamin120
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Comment: C: Advice on cluster hardware
... Ramon: That sounds like a tremendously exciting project! You seem to have done much research, and your solution should be both scalable and reasonably priced. I have seen reports that R is "compatible" with openMosix, but I have not found reports of real-world experience. Does R use shared memor ...
written 16.0 years ago by Michael Benjamin120
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Comment: C: From Limma to SAM
... Hi, all-- I wanted to start a thread on R speed/benchmarking. There is a nice R benchmarking overview at http://www.sciviews.org/other/benchmark.htm, along with a free script so you can see how your machine stacks up. Looks like R is substantially faster than S-plus. My problem is this: with 512 ...
written 16.0 years ago by Michael Benjamin120
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Comment: C: Re: Manova nuances
... This sounds very reasonable. I'm having a bit of trouble with the implementation. How do you solve for a variable? I know u * diag(d) * t(v) gets your original data, but how do you pick variables? Just taking the first four columns of u or v alone doesn't work--I tried. There must be a way to c ...
written 16.1 years ago by Michael Benjamin120
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Comment: C: Re: Manova nuances
... Can I do instead: comps1<-svd(teset[group1])$d comps2<-svd(teset[group2])$d t.test(comps1,comps2) Maybe I could just compare the top two or three components to one another? Mike -----Original Message----- From: Baker, Stephen [mailto:Stephen.Baker@umassmed.edu] Sent: Friday, November 21, 20 ...
written 16.1 years ago by Michael Benjamin120
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Comment: C: Re: Manova nuances
... Yes, Dr. Liaw is closer to my desired goal of one summary statistic for a large number of variables. Is that possible with PCA? I appreciate Dr. Baker's thoughts, though--I think PCA and manova have similarities. -----Original Message----- From: Liaw, Andy [mailto:andy_liaw@merck.com] Sent: Frida ...
written 16.1 years ago by Michael Benjamin120
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Answer: A: RE: Bioconductor Digest, Vol 9, Issue 28
... Anybody here using manova? It's powerful and pretty fast, but I'm finding that you can't have more variables than samples (limits its applicability to microarray research). Is there any way around this? Assume dim(eset) 1200 35 transeset<-t(eset) fit<-manova(transeset ~ categories) summa ...
written 16.1 years ago by Michael Benjamin120

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