Please ignore this message. ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Fri, 23 Mar 2007, Dick Beyer wrote: > Does anyone have the metadata files for the affy u133xp3 chip they'd like to > share? > > Thanks, > Dick > > ******************************************************************** *********** > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > ******************************************************************** *********** > > On Fri, 23 Mar 2007 bioconductor-request at stat.math.ethz.ch wrote: > >> Send Bioconductor mailing list submissions to >> bioconductor at stat.math.ethz.ch >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> or, via email, send a message with subject or body 'help' to >> bioconductor-request at stat.math.ethz.ch >> >> You can reach the person managing the list at >> bioconductor-owner at stat.math.ethz.ch >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Bioconductor digest..." >> >> >> Today's Topics: >> >> 1. LIMMA P-value calculations/Suggestions for flagged data >> (Gordon K Smyth) >> 2. Re: Solved: RE: Error in rowname in lumiR? (Seth Falcon) >> 3. plotDeg in affycoretools (claire wilson) >> 4. Re: plotDeg in affycoretools (James W. MacDonald) >> 5. Re: plotDeg in affycoretools (claire wilson) >> 6. Re: plotDeg in affycoretools (James W. MacDonald) >> 7. Re: CGH microarrays significance test (Jo?o Fadista) >> 8. Re: boot.phylo( ) function (Emmanuel Paradis) >> 9. Re: Error in rowname in lumiR? (Pan Du) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 22 Mar 2007 22:49:31 +1100 (EST) >> From: "Gordon K Smyth" <smyth at="" wehi.edu.au=""> >> Subject: [BioC] LIMMA P-value calculations/Suggestions for flagged >> data >> To: "Lance E. Palmer" <lance.palmer at="" stonybrook.edu=""> >> Cc: bioconductor at stat.math.ethz.ch >> Message-ID: >> <2962.58.106.100.90.1174564171.squirrel at homebase.wehi.edu.au> >> Content-Type: text/plain;charset=iso-8859-1 >> >>> Date: Wed, 21 Mar 2007 16:04:31 -0400 >>> From: "Lance E. Palmer" <lance.palmer at="" stonybrook.edu=""> >>> Subject: [BioC] LIMMA P-value calculations/Suggestions for flagged >>> data >>> To: bioconductor at stat.math.ethz.ch >>> >>> I just had a question/concern about P value calculations in Limma (I am >>> using latest version of Bioconductor) >>> >>> I recently ran 3 arrays through my analysis. The slides were analayzed >>> with Genepix software. There were a couple of genes that concerned me. >>> One had a log fold change of -3.765. The adjusted p-value (fdr) >>> was .027. I looked at the individual M values for the arrays and they >>> were -0.009336, 0.09217 and -3.765. >>> >>> I noticed that the first two arrays had a 'not found' flag. So >>> basically the analysis gave a significant P-value using only 1 piece of >>> data. Is this something that is correct? >> >> Yes, it is correct. If there is only one data value with weight>0 for a >> particular probe, then >> limma uses the empirical Bayes prior standard deviation for that probe to >> form a t-statistic. >> >> Think of it this way. You observed M=-3.765 for this probe. That's a large >> negative value. You >> know from looking at the other probes that the standard deviation of >> M-values is usually around >> 0.03, say, so -3.7 is very likely genuinely different from zero. >> >>> I also wonder if I should even remove 'not found' flagged data. >>> Originally I did not, but someone suggested I do. I originally did not >>> remove it because of the case listed above. >> >> I've argued on this mailing list and elsewhere for a long time that, rather >> than flagging faint >> spots, it's better to use a better background correction method that avoids >> a blow out of M-values >> at low intensities. >> >> Best wishes >> Gordon >> >>> However, the case above tells us something about the experiments. How >>> do people deal with this situation? >>> >>> -Lance Palmer >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 22 Mar 2007 06:19:27 -0700 >> From: Seth Falcon <sfalcon at="" fhcrc.org=""> >> Subject: Re: [BioC] Solved: RE: Error in rowname in lumiR? >> To: bioconductor at stat.math.ethz.ch >> Message-ID: <m2fy7x8lgg.fsf at="" ziti.fhcrc.org=""> >> Content-Type: text/plain; charset=iso-8859-1 >> >> Ingrid H. G. ?stensen <ingrid.h.g.ostensen at="" rr-research.no=""> writes: >> >>> Hi >>> >>> I got a tip regarding the error and now things work (so far....) >> >> In case someone else goes down the same path, can you tell us what the >> tip was? >> >> >> -- >> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >> http://bioconductor.org >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 22 Mar 2007 13:45:34 -0000 >> From: "claire wilson" <c.wilson at="" epistem.co.uk=""> >> Subject: [BioC] plotDeg in affycoretools >> To: <bioconductor at="" stat.math.ethz.ch=""> >> Message-ID: >> <dfdb9d8e7f453a4d9c29c66de3410d833ee7e8 at="" server.epistem.local=""> >> Content-Type: text/plain >> >> Hi all, >> >> am getting the following error when I call plotDeg from affycoretools, >> can anyone help me out? >> >> Many thanks >> >> claire >> >>> plotDeg(eset.f) >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "pm", for >> signature "exprSet" >> >> >> sessionInfo() >> R version 2.4.1 (2006-12-18) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >> Kingdom.1252;LC_MONETARY=English_United >> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >> "datasets" >> [8] "methods" "base" >> >> other attached packages: >> hgu133plus2cdf affycoretools biomaRt RCurl >> XML >> "1.14.0" "1.6.1" "1.8.2" "0.8-0" >> "1.6-0" >> GOstats Category genefilter survival >> KEGG >> "2.0.4" "2.0.3" "1.12.0" "2.30" >> "1.14.1" >> RBGL annotate GO graph >> limma >> "1.10.0" "1.12.1" "1.14.1" "1.12.1" >> "2.9.13" >> affy affyio Biobase >> "1.12.2" "1.2.0" "1.12.2" >> >> >> >> This message has been scanned for viruses by BlackSpider Mai...{{dropped}} >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Thu, 22 Mar 2007 09:52:43 -0400 >> From: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> >> Subject: Re: [BioC] plotDeg in affycoretools >> To: claire wilson <c.wilson at="" epistem.co.uk=""> >> Cc: bioconductor at stat.math.ethz.ch >> Message-ID: <46028A2B.5010704 at med.umich.edu> >> Content-Type: text/plain; charset="utf-8"; format=flowed >> >> Hi Claire, >> >> claire wilson wrote: >>> Hi all, >>> >>> am getting the following error when I call plotDeg from affycoretools, >>> can anyone help me out? >> >> It would appear that you are calling plotDeg() on an exprSet, rather >> than an AffyBatch. At the exprSet stage you have already computed >> expression values, so there are no longer any pm probes to plot. >> >> Best, >> >> Jim >> >> >>> >>> Many thanks >>> >>> claire >>> >>> >>>> plotDeg(eset.f) >>> >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function "pm", for >>> signature "exprSet" >>> >>> >>> sessionInfo() >>> R version 2.4.1 (2006-12-18) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >>> Kingdom.1252;LC_MONETARY=English_United >>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >>> >>> attached base packages: >>> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >>> "datasets" >>> [8] "methods" "base" >>> >>> other attached packages: >>> hgu133plus2cdf affycoretools biomaRt RCurl >>> XML >>> "1.14.0" "1.6.1" "1.8.2" "0.8-0" >>> "1.6-0" >>> GOstats Category genefilter survival >>> KEGG >>> "2.0.4" "2.0.3" "1.12.0" "2.30" >>> "1.14.1" >>> RBGL annotate GO graph >>> limma >>> "1.10.0" "1.12.1" "1.14.1" "1.12.1" >>> "2.9.13" >>> affy affyio Biobase >>> "1.12.2" "1.2.0" "1.12.2" >>> >>> >>> >>> This message has been scanned for viruses by BlackSpider Mai...{{dropped}} >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues. >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Thu, 22 Mar 2007 14:10:50 -0000 >> From: "claire wilson" <c.wilson at="" epistem.co.uk=""> >> Subject: Re: [BioC] plotDeg in affycoretools >> To: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> >> Cc: bioconductor at stat.math.ethz.ch >> Message-ID: >> <dfdb9d8e7f453a4d9c29c66de3410d833ee7ea at="" server.epistem.local=""> >> Content-Type: text/plain; charset="US-ASCII" >> >> Hi Jim, >> >> Many thanks for your prompt reply. I have used the affystart function to >> load the data into R. How do I access the raw data and not just the >> expression set. I would like to see the degradation and density plots, >> but only the PCA one remained. >> >> Kind Regards >> >> Claire >> >>> -----Original Message----- >>> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] >>> Sent: 22 March 2007 13:53 >>> To: claire wilson >>> Cc: bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] plotDeg in affycoretools >>> >>> Hi Claire, >>> >>> claire wilson wrote: >>>> Hi all, >>>> >>>> am getting the following error when I call plotDeg from >>> affycoretools, >>>> can anyone help me out? >>> >>> It would appear that you are calling plotDeg() on an exprSet, >>> rather than an AffyBatch. At the exprSet stage you have >>> already computed expression values, so there are no longer >>> any pm probes to plot. >>> >>> Best, >>> >>> Jim >>> >>> >>>> >>>> Many thanks >>>> >>>> claire >>>> >>>> >>>>> plotDeg(eset.f) >>>> >>>> Error in function (classes, fdef, mtable) : >>>> unable to find an inherited method for function "pm", for >>>> signature "exprSet" >>>> >>>> >>>> sessionInfo() >>>> R version 2.4.1 (2006-12-18) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >>>> Kingdom.1252;LC_MONETARY=English_United >>>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >>>> >>>> attached base packages: >>>> [1] "splines" "tools" "stats" "graphics" >>> "grDevices" "utils" >>>> "datasets" >>>> [8] "methods" "base" >>>> >>>> other attached packages: >>>> hgu133plus2cdf affycoretools biomaRt RCurl >>>> XML >>>> "1.14.0" "1.6.1" "1.8.2" "0.8-0" >>>> "1.6-0" >>>> GOstats Category genefilter survival >>>> KEGG >>>> "2.0.4" "2.0.3" "1.12.0" "2.30" >>>> "1.14.1" >>>> RBGL annotate GO graph >>>> limma >>>> "1.10.0" "1.12.1" "1.14.1" "1.12.1" >>>> "2.9.13" >>>> affy affyio Biobase >>>> "1.12.2" "1.2.0" "1.12.2" >>>> >>>> >>>> >>>> This message has been scanned for viruses by BlackSpider >>>> Mai...{{dropped}} >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Affymetrix and cDNA Microarray Core >>> University of Michigan Cancer Center >>> 1500 E. Medical Center Drive >>> 7410 CCGC >>> Ann Arbor MI 48109 >>> 734-647-5623 >>> >>> >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and >>> should not be used for urgent or sensitive issues. >>> >>> >>> >>> >> >> >> This message has been scanned for viruses by BlackSpider Mai...{{dropped}} >> >> >> >> ------------------------------ >> >> Message: 6 >> Date: Thu, 22 Mar 2007 10:51:30 -0400 >> From: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> >> Subject: Re: [BioC] plotDeg in affycoretools >> To: claire wilson <c.wilson at="" epistem.co.uk=""> >> Cc: bioconductor at stat.math.ethz.ch >> Message-ID: <460297F2.4060204 at med.umich.edu> >> Content-Type: text/plain; charset="utf-8"; format=flowed >> >> Hi Claire, >> >> The affystart() function should have dumped pdfs for all three plots in >> your working directory. Let me know if they are not there. >> >> I wrote affystart() for those situations where I am not doing the >> analysis. I just wanted to do some quick QA plots and compute expression >> values that I can send on to whomever is actually doing the work. So >> really, this is not the function you want for an interactive analysis. >> >> Instead something like this would work. >> >> dat <- ReadAffy() >> plotHist(dat) >> plotDeg(dat) >> eset <- rma(dat) >> plotPCA(eset) >> .. >> >> >> You might also take a look at the affyQCReport package, which will do >> some other QA stuff as well. >> >> Best, >> >> Jim >> >> claire wilson wrote: >>> Hi Jim, >>> >>> Many thanks for your prompt reply. I have used the affystart function to >>> load the data into R. How do I access the raw data and not just the >>> expression set. I would like to see the degradation and density plots, >>> but only the PCA one remained. >>> >>> Kind Regards >>> >>> Claire >>> >>> >>>> -----Original Message----- >>>> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] >>>> Sent: 22 March 2007 13:53 >>>> To: claire wilson >>>> Cc: bioconductor at stat.math.ethz.ch >>>> Subject: Re: [BioC] plotDeg in affycoretools >>>> >>>> Hi Claire, >>>> >>>> claire wilson wrote: >>>> >>>>> Hi all, >>>>> >>>>> am getting the following error when I call plotDeg from >>>> >>>> affycoretools, >>>> >>>>> can anyone help me out? >>>> >>>> It would appear that you are calling plotDeg() on an exprSet, >>>> rather than an AffyBatch. At the exprSet stage you have >>>> already computed expression values, so there are no longer >>>> any pm probes to plot. >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>>> >>>>> Many thanks >>>>> >>>>> claire >>>>> >>>>> >>>>> >>>>>> plotDeg(eset.f) >>>>> >>>>> Error in function (classes, fdef, mtable) : >>>>> unable to find an inherited method for function "pm", for >>>>> signature "exprSet" >>>>> >>>>> >>>>> sessionInfo() >>>>> R version 2.4.1 (2006-12-18) >>>>> i386-pc-mingw32 >>>>> >>>>> locale: >>>>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >>>>> Kingdom.1252;LC_MONETARY=English_United >>>>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >>>>> >>>>> attached base packages: >>>>> [1] "splines" "tools" "stats" "graphics" >>>> >>>> "grDevices" "utils" >>>> >>>>> "datasets" >>>>> [8] "methods" "base" >>>>> >>>>> other attached packages: >>>>> hgu133plus2cdf affycoretools biomaRt RCurl >>>>> XML >>>>> "1.14.0" "1.6.1" "1.8.2" "0.8-0" >>>>> "1.6-0" >>>>> GOstats Category genefilter survival >>>>> KEGG >>>>> "2.0.4" "2.0.3" "1.12.0" "2.30" >>>>> "1.14.1" >>>>> RBGL annotate GO graph >>>>> limma >>>>> "1.10.0" "1.12.1" "1.14.1" "1.12.1" >>>>> "2.9.13" >>>>> affy affyio Biobase >>>>> "1.12.2" "1.2.0" "1.12.2" >>>>> >>>>> >>>>> >>>>> This message has been scanned for viruses by BlackSpider >>>>> Mai...{{dropped}} >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> -- >>>> James W. MacDonald, M.S. >>>> Biostatistician >>>> Affymetrix and cDNA Microarray Core >>>> University of Michigan Cancer Center >>>> 1500 E. Medical Center Drive >>>> 7410 CCGC >>>> Ann Arbor MI 48109 >>>> 734-647-5623 >>>> >>>> >>>> ********************************************************** >>>> Electronic Mail is not secure, may not be read every day, and >>>> should not be used for urgent or sensitive issues. >>>> >>>> >>>> >>>> >>> >>> >>> >>> This message has been scanned for viruses by BlackSpider MailControl - >>> www.blackspider.com >> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues. >> >> >> >> ------------------------------ >> >> Message: 7 >> Date: Thu, 22 Mar 2007 16:49:56 +0100 >> From: Jo?o Fadista <joao.fadista at="" agrsci.dk=""> >> Subject: Re: [BioC] CGH microarrays significance test >> To: "Sean Davis" <sdavis2 at="" mail.nih.gov="">, >> <bioconductor at="" stat.math.ethz.ch=""> >> Cc: Ramon Diaz-Uriarte <rdiaz at="" cnio.es=""> >> Message-ID: >> <ea09c4b2b0f16e44b8f3311629493c0d02ed4e98 at="" djfpost01.djf.agrsci.dk=""> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear Sean and Ramon, >> >> Thanks for your thoughts of what should I do. I will try to digest your >> ideas. >> I got myself now the book "Mixed-effects models in S and S-plus" for helping >> me modelling my data. >> Wish me luck! >> >> Best regards >> >> Jo?o Fadista >> Ph.d. student >> >> >> UNIVERSITY OF AARHUS >> Faculty of Agricultural Sciences >> Research Centre Foulum >> Dept. of Genetics and Biotechnology >> Blichers All? 20, P.O. BOX 50 >> DK-8830 Tjele >> >> Phone: +45 8999 1900 >> Direct: +45 8999 1900 >> >> E-mail: Joao.Fadista at agrsci.dk >> Web: http://www.agrsci.org >> >> This email may contain information that is confidential. >> Any use or publication of this email without written permission from Faculty >> of Agricultural Sciences is not allowed. >> If you are not the intended recipient, please notify Faculty of Agricultural >> Sciences immediately and delete this email. >> >> >> >> -----Original Message----- >> From: Sean Davis [mailto:sdavis2 at mail.nih.gov] >> Sent: Wednesday, March 21, 2007 5:40 PM >> To: bioconductor at stat.math.ethz.ch >> Cc: Ramon Diaz-Uriarte; Jo?o Fadista >> Subject: Re: [BioC] CGH microarrays significance test >> >> On Wednesday 21 March 2007 12:06, Ramon Diaz-Uriarte wrote: >>> Dear Joao, >>> >>> On Wednesday 21 March 2007 16:33, Jo?o Fadista wrote: >>>> Dear list, >>>> >>>> I have a CGH microarray experiment where I compare male vs. female >>>> in each sample (3 technical replicates with dye swaps = 6 samples). >>>> So in theory I would expect to see a difference in log2ratios of the >>>> X chromosome compared to the autosomes. This experiment is made >>>> mainly to assess/optimize the reliability of the protocol and the >>>> in-house microarray platform for CGH microarrays experiments. >> >> A very useful measure for CGH when comparing protocols, etc., is a measure >> of signal divided by a measure of noise (signal-to-noise ratio). You could >> use a very simple measure like the mean or median of the X chromosome minus >> the mean/median of the autosomes as the signal and then the sd or MAD of the >> autosomes as the noise. Each array can then be summarized by a single >> number. Coming up with a statistical test is quite interesting, but I don't >> think it is necessary for what you are describing. >> >> As with all microarray analyses, there is no substitute for visualizing the >> data, doing adequate preprocessing (you can't just loess-normalize the >> arrays as you would with expression arrays), and generating quality-control >> plots. >> >> Sean >> >> >> >> ------------------------------ >> >> Message: 8 >> Date: Thu, 22 Mar 2007 04:15:55 -0400 >> From: Emmanuel Paradis <paradis at="" isem.univ-montp2.fr=""> >> Subject: Re: [BioC] boot.phylo( ) function >> To: bioconductor at stat.math.ethz.ch >> Message-ID: <46023B3B.9080904 at isem.univ-montp2.fr> >> Content-Type: text/plain; charset=us-ascii; format=flowed >> >> Dear all, >> >> I have replied privately to this query, mentioning that the BioC list >> may not be appropriate for this kind of question, but I was apparently >> wrong (I'm not on the list, so not aware of the usual topics). >> >> Martin Morgan wrote: >>> Hi Nora -- >>> >>> I do not have direct experience with this package, but from the help >>> page >>> >>>> library(ape) >>>> ?boot.phylo >>> >>> perhaps >>> >>> allbacteria <- read.dna("allbacteriafasta","fasta") >>> distallbacteria <- >>> dist.dna(allbacteria, pairwise.deletion=TRUE, as.matrix=TRUE) >>> njtree <- nj(distallbacteria) >>> >>> boot.phylo(njtree, >>> allbacteria, >>> FUN=function(bootstrappedData) { >>> nj(dist.dna(bootstrappedData, >>> pairwise.deletion=TRUE, >>> as.matrix=TRUE)) >>> }) >>> >>> works? >> >> Yes, this is it. The option as.matrix=TRUE is not needed, and will >> likely slow down the whole thing. >> >> Earl Glynn asked me for an example of using boot.phylo with a "toy" >> problem. Here's what can be done in R: >> >> library(ape) >> data(woodmouse) >> d <- dist.dna(woodmouse) >> tr <- nj(d) >> bp <- boot.phylo(tr, woodmouse, function(xx) nj(dist.dna(xx))) >> plot(tr) >> nodelabels(bp) >> >> Then you can change the options of dist.dna and boot.phylo to see how >> this may affect the results. There is a more "real life" example in my >> book "APER" (this case study is actually spread in several chapters, so >> that it explains the analysis from A to Z, or nearly). >> >> boot.phylo is fairly fast for small to moderate size, on my laptop I have: >> >> > system.time(bp <- boot.phylo(tr, woodmouse, function(xx) >> nj(dist.dna(xx)))) >> [1] 11.089 0.008 11.098 0.000 0.000 >> >> These times are expected to be quite longer for big data sets as a >> substantial part of the computation is done in R (I plan to rewrite this >> in C sometime). Also I have experimental codes for dist.dna that are >> much faster than the current ones. >> >>> Martin >>> >>> Nora Muda <noramuda at="" yahoo.com=""> writes: >>> >>>> Dear BioConducter useRs, >>>> >>>> I have problems in writing boot.phylo() function. >>>> >>>> Let say I have 30 aligned sequences; then I computed >>>> pairwise distances with "K80" method. Then I construct >>>> phylogenetic tree with neighbor-joining method and my >>>> proposed method. Now I have problems in writing "FUN" >>>> in boot.phylo() function. Below are examples of my >>>> programs: >>>> >>>> library(ape) >>>> allbacteria <- read.dna("allbacteriafasta","fasta") >>>> distallbacteria <- >>>> dist.dna(allbacteria,pairwise.deletion=TRUE,as.matrix=TRUE) >>>> plot(nj(distallbacteria)) >>>> >>>> boot.phylo(plot(nj(distallbacteria)),allbacteria,nj(distallbacteria)) >>>> >>>> What should I put as FUN in boot.phylo? >>>> >>>> I make comparison between distances of "K80" in PHYLIP >>>> and dist.dna("K80").There are a lot of differences esp >>>> in PHYLIP there is a default for >>>> transversion/transition rate; which is 2 but not in >>>> ape package. How to modify it to make it the same? >> >> Here the answer I sent to Nora: >> >> Indeed, and these differences are expected. PHYLIP assumes a >> "theoretically expected" value of the ts/tv ratio, the distance is then >> calculated by maximizing a likelihood function. (I owe this information >> to my colleague Olivier Gascuel who dissected PHYLIP's code.) You can >> change the default of the ts/tv ratio, in which case it is also >> estimated by ML. dist.dna is faithful to Kimura's original formulae; it >> also computes the variance of the distances (which PHYLIP does not). >> >> Emmanuel Paradis >> >> >> >> ------------------------------ >> >> Message: 9 >> Date: Thu, 22 Mar 2007 16:32:19 -0500 >> From: Pan Du <dupan at="" northwestern.edu=""> >> Subject: Re: [BioC] Error in rowname in lumiR? >> To: <ingrid.h.g.ostensen at="" rr-research.no=""> >> Cc: Simon Lin <s-lin2 at="" northwestern.edu="">, >> bioconductor at stat.math.ethz.ch >> Message-ID: <c2286013.3339%dupan at="" northwestern.edu=""> >> Content-Type: text/plain; charset="ISO-8859-1" >> >> Hi Ingrid, >> >> You need to update the lumi package. This problem should have been solved. >> The current version of lumi is 1.0.10. >> >> Version 1.1.0 will be released next week, which will include several new >> features, including support of BeadStudio 3.0 format, adding a lumiB >> function to allow user adding background correction and a lumiExpresso >> function to encapsulate all the preprocessing functions. A QC slot will be >> added in the LumiBatch class and the LumiQC class will be removed. >> >> Thanks! >> >> >> Pan >> >> >> -------- Original Message -------- >> Subject: [BioC] Error in rowname in lumiR? >> Date: Thu, 22 Mar 2007 09:31:50 +0100 >> From: Ingrid H. G. ?stensen <ingrid.h.g.ostensen at="" rr-research.no=""> >> To: <bioconductor at="" stat.math.ethz.ch=""> >> >> Hi >> >> I posted a message yesterday regarding the lumi package. I have been >> looking at the code for the lumiR procedure and found the line were >> things are going wrong: >> >> rownames(allData) <- targetID >> >> The error message that comes is: >> >> Error in `row.names<-.data.frame`(`*tmp*`, value = c("ILMN_10000", >> "ILMN_100000", : duplicate 'row.names' are not allowed >> >> Is seems that rownames can not see the difference between the different >> Illumina target ID?s, example of ID: >> >> ILMN_10000 >> ILMN_100000 >> ILMN_100007 >> ILMN_100009 >> ILMN_10001 >> ILMN_100010 >> ILMN_10002 >> ILMN_100028 >> ILMN_100030 >> ILMN_100031 >> ILMN_100034 >> ILMN_100037 >> ILMN_10004 >> ILMN_10005 >> ILMN_100054 >> ILMN_100059 >> ILMN_10006 >> ILMN_100075 >> ILMN_100079 >> ILMN_100083 >> ILMN_100084 >> ILMN_100086 >> ILMN_10009 >> ILMN_100091 >> ILMN_100097 >> ILMN_1001 >> ILMN_10010 >> ILMN_100101 >> ILMN_100106 >> ILMN_10011 >> ILMN_100114 >> ILMN_10012 >> >> >> More information: >> >> class(allData) >> [1] "data.frame" >> >> class(targetID) >> [1] "character" >> >> sessionInfo() >> R version 2.4.1 (2006-12-18) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=Norwegian (Bokm?l)_Norway.1252;LC_CTYPE=Norwegian >> (Bokm?l)_Norway.1252;LC_MONETARY=Norwegian >> (Bokm?l)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokm?l)_Norway.1252 >> >> attached base packages: >> [1] "tools" "stats" "graphics" "grDevices" "utils" >> "datasets" "methods" "base" >> >> other attached packages: >> xtable RColorBrewer limma lumi mgcv >> affy affyio Biobase >> "1.4-3" "0.2-3" "2.9.13" "1.0.3" "1.3-23" >> "1.12.2" "1.2.0" "1.12.2" >> >> Does anyone have any suggestions about what might be wrong, can it be >> because I use R 2.4.1 and the package is for R 2.5.x? Or can it be >> something with the data file that contains the Illumina data. >> >> >> Regards, >> Ingrid >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> End of Bioconductor Digest, Vol 49, Issue 22 >> ******************************************** >> > > >