Question

matchprobes vignette?

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Michael Seewald ▴ 130

@michael-seewald-574

Last seen 10.3 years ago

Dear Wolfgang, dear Robert, It seems that the vignette of matchprobes is broken. I am using 1.9.1 alpha (2004-05-25) and matchprobes 1.0.8. This is what I get: > library(affy) > library(matchprobes) > openVignette() Please select (by number) a vignette 1: Handling probe sequence information 2: Biobase Primer 3: Howto Bioconductor 4: HowTo HowTo 5: esApply Introduction Selection: 1 Error in switch(ext[length(ext)], pdf = openPDF(vigFiles[index]), html = browseURL(paste("file://", : Don't know how to handle this vignette > Any help is appreciated! Thanks a lot & best wishes, Michael

probe Biobase matchprobes probe Biobase matchprobes • 1.4k views

ADD COMMENT • link updated 20.5 years ago by Jeff Gentry ★ 3.9k • written 20.5 years ago by Michael Seewald ▴ 130

score 0 · Answer 1 · 2004-06-16

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James Wettenhall ▴ 1000

@james-wettenhall-153

Last seen 10.3 years ago

On Wed, 16 Jun 2004, Michael Seewald wrote: > It seems that the vignette of matchprobes is broken. I am using 1.9.1 alpha I don't know much about openVignette(), but I can access matchprobes.pdf without any problems at: http://www.bioconductor.org/repository/devel/vignette/matchprobes.pdf or using: browseURL(file.path(system.file("doc",package="matchprobes"),"matchpro bes.pdf")) Hope this helps, James

ADD COMMENT • link 20.5 years ago James Wettenhall ▴ 1000

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On Thu, 17 Jun 2004, James Wettenhall wrote: > http://www.bioconductor.org/repository/devel/vignette/matchprobes.pdf Got it, thanks! > browseURL(file.path(system.file("doc",package="matchprobes"),"matchp robes.pdf")) Nope, that didn't work. > Hope this helps, Thanks! Michael

ADD REPLY • link 20.5 years ago Michael Seewald ▴ 130

score 0 · Answer 2 · 2004-06-16

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Jeff Gentry ★ 3.9k

@jeff-gentry-12

Last seen 10.3 years ago

> It seems that the vignette of matchprobes is broken. I am using 1.9.1 alpha > (2004-05-25) and matchprobes 1.0.8. This is what I get: Hello ... It looks like the matchprobes vignette was still using a 'multiget' call, which was removed in favor of 'mget' in BioC-Devel. I thought I had rooted out all instances of multiget, but this one must have snuck through somehow. I have fixed this with verison 1.0.9. Sorry for the confusion, -J

ADD COMMENT • link 20.5 years ago Jeff Gentry ★ 3.9k

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Hi Jeff, in fact the .tar.gz file for the vsn package that is linked under http://www.bioconductor.org/repository/release1.4/package/html/vsn.htm l also does not contain a vignette. The .zip file, however, does. Can you replace the .tar.gz file by one that built correctly? (From the files that are left over in the inst/doc directory of that tar-ball, it appears that Sweave terminated when it encountered a call to affy::expresso, and I recall that there was a short period during the run-up to the release when affy wasn't working) Best wishes Wolfgang Jeff Gentry wrote: >>It seems that the vignette of matchprobes is broken. I am using 1.9.1 alpha >>(2004-05-25) and matchprobes 1.0.8. This is what I get: > > > Hello ... > > It looks like the matchprobes vignette was still using a 'multiget' call, > which was removed in favor of 'mget' in BioC-Devel. I thought I had > rooted out all instances of multiget, but this one must have snuck through > somehow. I have fixed this with verison 1.0.9. > > Sorry for the confusion, > -J > -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber

ADD REPLY • link 20.5 years ago Wolfgang Huber ★ 13k

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> in fact the .tar.gz file for the vsn package that is linked under > http://www.bioconductor.org/repository/release1.4/package/html/vsn.h tml > also does not contain a vignette. The .zip file, however, does. > Can you replace the .tar.gz file by one that built correctly? I actually had just fixed this an hour or so ago, so all should be well.

ADD REPLY • link 20.5 years ago Jeff Gentry ★ 3.9k

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I have installed R version 1.9 (64 bit compiled) and the Biocunductor packages release 1.4 which include the vsn package 1.4.13 and I am getting the following error: data <- ReadAffy(filenames=cels, sampleNames=names, verbose=F) > vsn.data <- expresso(data, normalize.method="vsn", bg.correct=F, pmcorrect.method="pmonly", summary.method="medianpolish") normalization: vsn PM/MM correction : pmonly expression values: medianpolish normalizing...vsn: 20000 x 24 matrix (1 stratum). Please wait for 4 dots: Error: L-BFGS-B needs finite values of fn Execution halted Isaac

ADD REPLY • link 20.5 years ago Isaac Neuhaus ▴ 360

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Hi Isaac, vsn uses a maximum-likelihood method for the parameter estimation, and since the log-likelihood is not quadratic, it uses the numeric optimizer "L-BFGS-B". As far as I can see, the log-likelihood is concave, i.e. has only one maximum, for practically all data sets. But for odd data sets and with bad start values, the numeric optimizer can run off into nirwana before finding the maximum. That seems to happen in your case. Can you try the following: 1. Look at scatterplots of the probe intensities between all (or at least many) pairs of chips, and see if there's anything odd: for(i in 2:24) for (j in 1:(i-1)) { plot(exprs(data)[, c(i,j)], pch=".", main=paste(i,j)) locator(n=1) } 2. Try to use different (non-default) start parameters, e.g. pstart <- array(c(rep(0, 24), rep(1,24)), dim=c(1,24,2)) vsn.data <- expresso(data, normalize.method="vsn", normalize.param(list(pstart=pstart)), bg.correct=FALSE, pmcorrect.method="pmonly", summary.method="medianpolish") 3. For a better diagnosis, I would have to lok at your data. I will be off email for the next two weeks, but please let me know after that (July) - I would be interested in making vsn more robust e.g. by having a smarter guess at the start parameters. Best wishes Wolfgang Isaac Neuhaus wrote: > I have installed R version 1.9 (64 bit compiled) and the Biocunductor > packages release 1.4 which include the vsn package 1.4.13 and I am > getting the following error: > > data <- ReadAffy(filenames=cels, sampleNames=names, verbose=F) > > vsn.data <- expresso(data, normalize.method="vsn", bg.correct=F, > pmcorrect.method="pmonly", summary.method="medianpolish") > normalization: vsn > PM/MM correction : pmonly > expression values: medianpolish > normalizing...vsn: 20000 x 24 matrix (1 stratum). Please wait for 4 > dots: Error: L-BFGS-B needs finite values of fn > Execution halted > > Isaac > -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber

ADD REPLY • link 20.5 years ago Wolfgang Huber ★ 13k