[BioC] affy u133x3p chip
Dick Beyer
dbeyer at u.washington.edu
Sat Mar 24 00:39:20 CET 2007
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:
>
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>>
>> 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]]
>>
>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
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>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>
>> End of Bioconductor Digest, Vol 49, Issue 22
>> ********************************************
>>
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