Dear BioC Users, Does anyone have a reference for (or a good definition of) median- interquartile normalization? Is it the same as interquartile normalization? (If not, I would like a reference/definition of both) I have looked for such a definition in the literature, but I haven't found a satisfactory one. Thank you, Monnie McGee Monnie McGee, Ph.D. Associate Professor Department of Statistical Science Southern Methodist University Ph: 214-768-2462 Fax: 214-768-4035 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of bioconductor-request@stat.math.ethz.ch Sent: Thu 11/8/2007 5:00 AM To: bioconductor at stat.math.ethz.ch Subject: Bioconductor Digest, Vol 57, Issue 8 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. Re: Limma and Imagene flags (Leonardo Rocha) 2. Re: Problem running eBayes/lmFit (smohapat at vbi.vt.edu) 3. Combine dataset from different chip (Tom) 4. Re: Problem running eBayes/lmFit (elliott harrison) 5. Re: Affymetrix reannotation (Samuel Wuest) 6. Limma: how to combine duplicateCorrelation, dyeeffect and arrayweights? (dorthe.belgardt at medisin.uio.no) 7. Re: how to build a GOstats-compatible annotation package for plasmodium falciparum? (Marc Carlson) 8. Re: Affymetrix reannotation (James W. MacDonald) 9. GOTERM (Mete Civelek) 10. Question about a packages not yet in Bioconductor: AffyProbeMiner in R260 under windows (phguardiol at aol.com) 11. Re: GOTERM (Robert Gentleman) 12. Re: Question about a packages not yet in Bioconductor: AffyProbeMiner in R260 under windows (Robert Gentleman) 13. Re : Question about reannotated Affy annotation files - Question about AffyProbeMiner in R260 under windows (phguardiol at aol.com) 14. Re: Re : Question about reannotated Affy annotation files - Question about AffyProbeMiner in R260 under windows (Jarno Tuimala) 15. optimizazion cluster in Heatmap (Alessandro Fazio) ---------------------------------------------------------------------- Message: 1 Date: Wed, 7 Nov 2007 21:02:22 -0200 From: "Leonardo Rocha" <leobernardesrocha@gmail.com> Subject: Re: [BioC] Limma and Imagene flags To: <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <002001c82192$434cfd40$2d6691c8 at Biela> Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Hello Sally, You should try the following commands: myfun <- function(x) as.numeric(x$Flag ==0) RG <- read.imagene(filenames$target, wt.fun=myfun) I hope it helps. Good luck. Leonardo ----- Original Message ----- From: "Sally" <sagoldes@shaw.ca> To: <bioconductor at="" stat.math.ethz.ch=""> Sent: Tuesday, November 06, 2007 9:36 PM Subject: Re: [BioC] Limma and Imagene flags > >From reading the Limma User's Guide it says that a flag value of 0 means > >that Limma considers this a "bad spot" and removes data flagged 0 from > >subsequent preprocessing. But in Imagene a flag value of 0 means that > >this is a "good spot". How do you get around this? > > > Sally > [[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 ------------------------------ Message: 2 Date: Wed, 7 Nov 2007 07:07:02 -0500 (EST) From: smohapat@vbi.vt.edu Subject: Re: [BioC] Problem running eBayes/lmFit To: "elliott harrison" <e.harrison at="" epistem.co.uk=""> Cc: bioconductor at stat.math.ethz.ch Message-ID: <50466.71.171.41.163.1194437222.squirrel at webmail.vbi.vt.edu> Content-Type: text/plain;charset=iso-8859-1 Hello Elliott: I am trying to understand the problem here. From the design: > A9802 A9811 A9813 A9842 SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4 > 1 0 0 0 0 1 0 0 0 > 2 0 0 0 0 0 1 0 0 > 3 0 0 0 0 0 0 1 0 > 4 0 0 0 0 0 0 0 1 > 5 1 0 0 0 0 0 0 0 > 6 0 1 0 0 0 0 0 0 > 7 0 0 1 0 0 0 0 0 > 8 0 0 0 1 0 0 0 0 I understand that there is one sample of A9802(#5) and another of SAMPLE1 (#1). In the contrasts, these two groups are compared (OneVOne): > makeContrasts(OneVOne="A9802-SAMPLE1",OneVTwo="A9802-A9811",TwoVOne= "SAM > PLE1-SAMPLE2",levels=design) > I guess that because of the number of samples in each group being one, it is not possible to calculate variance, and hence the error message. This is how I understood Gordon's earlier post (https://stat.ethz.ch/pipermail/bioconductor/2005-May/009056.html): ------------ The "no residual degrees of freedom" message occurs because you have filtered out so many spots (by setting the weight to 0) that you have no more than one spot left for any of the probes. Hence there is no replication left in your experiment. No estimate of variability can be made and no statistical analysis can be done. ------------- If anyone knows more clearly, please elaborate. Saroj > The matrix seems to be doing what I want > > >> cont.matrix > Contrasts > Levels OneVOne OneVTwo TwoVOne > A9802 1 1 0 > A9811 0 -1 0 > A9813 0 0 0 > A9842 0 0 0 > SAMPLE1 -1 0 1 > SAMPLE2 0 0 -1 > SAMPLE3 0 0 0 > SAMPLE4 0 0 0 > > >> fit2 <- contrasts.fit(fit, cont.matrix) fit2 <- eBayes(fit2) > Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = > stdev.coef.lim) : No residual degrees of freedom in linear model fits > > > I've found a post that says this error message occurs because all data > is weighted out. I've checked the data after it is loaded, after > backgroundCorrect and it does not appear to be. Beyond that I doesn't look > like the normalizeBetweenArrays of RTotalbg$R RTRN has any weights. So I > must not be setting up the design matrix correctly? > > Any and all clues as to where I'm going wrong greatly appreciated. > > > > Elliott Harrison > > > > > > This message has been scanned for viruses by BlackSpider...{{dropped:3}} > > > _______________________________________________ > 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 > > ------------------------------ Message: 3 Date: Wed, 7 Nov 2007 12:04:07 +0000 (UTC) From: Tom <tomnovy@email.it> Subject: [BioC] Combine dataset from different chip To: bioconductor at stat.math.ethz.ch Message-ID: <loom.20071107t114711-812 at="" post.gmane.org=""> Content-Type: text/plain; charset=us-ascii Hi, I'm trying to merge the data comes from two different microarray chips (hgu133a and HThgu133a). I have seen that a lot of probe sets are in common in the two chip. Have you any suggestion?? ------------------------------ Message: 4 Date: Wed, 7 Nov 2007 12:15:43 -0000 From: "elliott harrison" <e.harrison@epistem.co.uk> Subject: Re: [BioC] Problem running eBayes/lmFit To: <smohapat at="" vbi.vt.edu=""> Cc: bioconductor at stat.math.ethz.ch Message-ID: <dfdb9d8e7f453a4d9c29c66de3410d835b1da7 at="" server.epistem.local=""> Content-Type: text/plain; charset="us-ascii" Hi Saroj, I see so multiple arrays in each group are needed. So I'll need to do some simpler test between the 2 arrays? Any suggestions? Thanks Elliott -----Original Message----- From: smohapat@vbi.vt.edu [mailto:smohapat@vbi.vt.edu] Sent: Wednesday, November 07, 2007 12:07 PM To: elliott harrison Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Problem running eBayes/lmFit Hello Elliott: I am trying to understand the problem here. From the design: > A9802 A9811 A9813 A9842 SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4 > 1 0 0 0 0 1 0 0 0 > 2 0 0 0 0 0 1 0 0 > 3 0 0 0 0 0 0 1 0 > 4 0 0 0 0 0 0 0 1 > 5 1 0 0 0 0 0 0 0 > 6 0 1 0 0 0 0 0 0 > 7 0 0 1 0 0 0 0 0 > 8 0 0 0 1 0 0 0 0 I understand that there is one sample of A9802(#5) and another of SAMPLE1 (#1). In the contrasts, these two groups are compared (OneVOne): > makeContrasts(OneVOne="A9802-SAMPLE1",OneVTwo="A9802-A9811",TwoVOne="S > AM > PLE1-SAMPLE2",levels=design) > I guess that because of the number of samples in each group being one, it is not possible to calculate variance, and hence the error message. This is how I understood Gordon's earlier post (https://stat.ethz.ch/pipermail/bioconductor/2005-May/009056.html): ------------ The "no residual degrees of freedom" message occurs because you have filtered out so many spots (by setting the weight to 0) that you have no more than one spot left for any of the probes. Hence there is no replication left in your experiment. No estimate of variability can be made and no statistical analysis can be done. ------------- If anyone knows more clearly, please elaborate. Saroj > The matrix seems to be doing what I want > > >> cont.matrix > Contrasts > Levels OneVOne OneVTwo TwoVOne > A9802 1 1 0 > A9811 0 -1 0 > A9813 0 0 0 > A9842 0 0 0 > SAMPLE1 -1 0 1 > SAMPLE2 0 0 -1 > SAMPLE3 0 0 0 > SAMPLE4 0 0 0 > > >> fit2 <- contrasts.fit(fit, cont.matrix) fit2 <- eBayes(fit2) > Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = > stdev.coef.lim) : No residual degrees of freedom in linear model fits > > > I've found a post that says this error message occurs because all data > is weighted out. I've checked the data after it is loaded, after > backgroundCorrect and it does not appear to be. Beyond that I doesn't > look like the normalizeBetweenArrays of RTotalbg$R RTRN has any > weights. So I must not be setting up the design matrix correctly? > > Any and all clues as to where I'm going wrong greatly appreciated. > > > > Elliott Harrison > > > > > > This message has been scanned for viruses by > BlackSpider...{{dropped:3}} > > > _______________________________________________ > 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 > > ------------------------------ Message: 5 Date: Wed, 07 Nov 2007 15:45:20 +0100 From: "Samuel Wuest" <swuest@botinst.uzh.ch> Subject: Re: [BioC] Affymetrix reannotation To: Marc Carlson <mcarlson at="" fhcrc.org=""> Cc: Bioconductor at stat.math.ethz.ch Message-ID: <web-10826981 at="" idmailbe2b.unizh.ch=""> Content-Type: text/plain;charset=iso-8859-1;format="flowed" Thanks a lot, I am familiar with the ath1121501 package. Now I don?t know whether it contains informations on the probe-level rather than on the probeset- level (e.g. whether a designed probe still targets an updated gene model? or which probe-sets are obsolete and can be considered to be outdated?) And: How can I retrieve such information without writing a blast- script to check every single probe against the most updated cDNA database? Thanks for any help on this. Samuel On Tue, 06 Nov 2007 10:31:38 -0800 Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Samuel Wuest wrote: >> Hi, >> >> I trying to assess a modified version of the Affymetrix present/absent >>call >> algorithm on my data, which have been generated from two-round amplified >>RNA >> hybridized to the Arabidopsis ATH1 GeneChip. >> >> I would need some negative control probesets, and thought of probesets >>that >> were designed based on wrong gene annotations (similar to what was used in >> the PANP method from Peter Warren et al.). >> Therefore, I wondered whether someone does a reannotation of Affy >>probesets >> on a regular base? (for example, the version 7 of the Arabidopsis Genome >> Annotation has been released recently, and some probesets on the AffyChip >> are most probably not matching any gene model anymore). >> >> If yes, where could I find the updated datafiles? Is there anything in the >> BioC annotation package for the ATH1Chip? >> >> Thanks for any help. >> Best, Sam >> >> ----------------------------------------------------- >> Dipl. Bot. Samuel Wust >> Dep. of Developmental Genetics >> Institute for Plant Biology >> University of Zuerich >> Zollikerstrasse 107 >> CH - 8008 Z?rich >> Phone: +41-(0)44 634 82 42 >> Mobile: + 41 (0)76 501 69 22 >> Email: swuest at botinst.uzh.ch >> >> _______________________________________________ >> 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 >> >> > > We provide a "standard" annotation package for this chip. You can find > it here: > > http://bioconductor.org/packages/2.1/data/annotation/html/ath1121501 .db.html > > > Marc > ------------------------------ Message: 6 Date: Wed, 7 Nov 2007 17:21:09 +0100 (CET) From: dorthe.belgardt@medisin.uio.no Subject: [BioC] Limma: how to combine duplicateCorrelation, dyeeffect and arrayweights? To: bioconductor at stat.math.ethz.ch Message-ID: <1667.129.240.47.68.1194452469.squirrel at webmail.uio.no> Content-Type: text/plain;charset=iso-8859-1 Hi, I am quite insecure if some parts of the analyis I did in Limma are really correct and I would highly appreciate if someone could take a look and give advice. My main concern is that I may not use the duplicatecorrelation, dyeeffect,arrayweights and spotweights correctly. The arrays I use are printed in duplicates with a spacing of 15000 (so 30000 features in total), and I did the imageprocessing in GenePixPro6.1. Thereby I flagged all spots close to backgroundsignal and with a rgn r2 <0.5 bad, and only 30% of my data remain unflagged. And this is what I did using Limma: > targets=readTargets("Targets_basicSat.txt") > targets SlideNumber FileName Cy3 Cy5 1 1 3096_basicSat.gpr ref A 2 2 3079_basicSat.gpr A ref 3 3 3089_basicSat.gpr ref A 4 4 3081_basicSat.gpr A ref 5 5 3071_basicSat.gpr ref B 6 6 3082_basicSat.gpr B ref 7 7 3085_basicSat.gpr ref B 8 8 8268_basicSat.gpr B ref 9 9 7829_basicSat.gpr ref C 10 10 3086_basicSat.gpr C ref 11 11 7823_basicSat.gpr ref C 12 12 7826_basicSat.gpr C ref 13 13 3090_basicSat.gpr ref D 14 14 3091_basicSat.gpr D ref 15 15 3092_basicSat.gpr ref D 16 16 7827_basicSat.gpr D ref Every other slide is a dyeswapped technical replicate and per "group" (A,B,C,D) there are 2 biological replicates. > K=read.maimages(targets$FileName, source="genepix.median", wt.fun=wtflags(0)) > types=readSpotTypes("SpottypesGAPDH.txt") > Status=controlStatus(types, K) > K$genes$Status=Status > K3=backgroundCorrect(K, method=?normexp?, offset=50) > K3=normalizeWithinArrays(K3, method="median") > K3a=normalizeBetweenArrays(K3, method="quantile") > design=modelMatrix(targets, ref="ref") > design A B C D [1,] 1 0 0 0 [2,] -1 0 0 0 [3,] 1 0 0 0 [4,] -1 0 0 0 [5,] 0 1 0 0 [6,] 0 -1 0 0 [7,] 0 1 0 0 [8,] 0 -1 0 0 [9,] 0 0 1 0 [10,] 0 0 -1 0 [11,] 0 0 1 0 [12,] 0 0 -1 0 [13,] 0 0 0 1 [14,] 0 0 0 -1 [15,] 0 0 0 1 [16,] 0 0 0 -1 Since I am expecting a non-negligible dyeeffect I created an other designmatrix and the following contrastMatrix: >design1=cbind(DyeEffect=1, design) >design.cont=makeContrasts("A", ?B?, ?A-B", levels=design1) Next I estimate the correlation of within-array-duplicates: >cor=duplicateCorrelation(K3b, design=design1, ndups=2, spacing=15000, weights=K3b$weights) My first question is: is it correct to use here the designmatrix for the dyeeffect (design1 in this case)? When fitting the linear model, I also want to use arrayweights, combined with spotweights. So I gave following commands: > aw=arrayWeights(K3b, design=design1) > w=matvec(K3b$weights, aw) Again the question: is it correct to use here the "design1"-matrix considering the dyeeffect? Then I fit the linear model: >fit=lmFit(K3b, design=design1, ndups=2, spacing=15000, cor=cor$consensus, weights=w) >fit1=contrasts.fit(fit, design.cont) >eb=eBayes(fit1) Another thing I am worried about is that taking into account the dyeeffect plus arrayweights plus spotweights might be a bit "too much"? Like in a way "overtransforming" my data? Especially since approx 70% of my data have a spotweight of zero. Might it be better to use the spotweight of 0,1 for bad spots, so that I do not loose the data completely? My apologies for this long email, I tried hard to find out the answers for myself reading the limmaguide and lots of other documents I found googleing, but still feel quite "stuck" in my analysis process. Thanks very much for any kind of help in advance! Best regards Dorthe -- Dorthe Belgardt Institute of Basic Medical Sciences Department of Physiology P.O. Box 1103 Blindern 0317 Oslo Norway ------------------------------ Message: 7 Date: Wed, 07 Nov 2007 10:47:54 -0800 From: Marc Carlson <mcarlson@fhcrc.org> Subject: Re: [BioC] how to build a GOstats-compatible annotation package for plasmodium falciparum? To: Paul Shannon <pshannon at="" systemsbiology.org=""> Cc: bioc <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <4732085A.9040907 at fhcrc.org> Content-Type: text/plain; charset=ISO-8859-1 Paul Shannon wrote: > Hi Marc, > > It sounds like you have your hands full! > > Would it be crazy if we were to undertake this ourselves, at the SBRI? > I am thinking of an organism-based package (like YEAST) rather than > a chip-specific package. > > Does the new pipeline create annotation packages which work with > GOstats and GSEA? > > - Paul > > > On Nov 6, 2007, at 4:41 PM, Marc Carlson wrote: > >> Well I plan to do this. But it's just not going to happen overnight. I >> am booked right now with a homology implementation and I also have to >> finish getting part of the promised pipeline in place for our other >> annotation package collaborators so that they can update their packages >> to the newer format for the upcoming release. This means that I may not >> get to start this for a couple of months, but it has been added to my >> todo list. >> >> For now, I recommend that you try to use the AnnBuilder package. We are >> planning to retire this package along with the style of annotation >> package that it spawns so this is definitely NOT a good long term >> solution and is to be used for the short term ONLY. But I think that it >> will probably get you the quick fix that you need. >> >> http://bioconductor.org/packages/2.1/bioc/html/AnnBuilder.html >> >> >> Marc Yes I am a very busy guy. I would love to collaborate with you on this. But I don't think that making a new package from scratch would be a very efficient use of your time. That is, there are good reasons why its going to take me a little while to get it to you. There are a lot of things to do. I agree that an organism based package is what is called for here and that is what I was planning to work on. As for your immediate needs, all you should need for GO stats or GSEA is an environment which you could make for yourself from the appropriate information. I can give you those parts in an unformated form if you want them. To format them into a proper environment you should only need to wrap them up in one. #Lets suppose that we rip off some of the info from the YEAST package to see how this would work: library(YEAST) res=mget(ls(YEASTGO), YEASTGO) #Then we could quickly make a couple quick fakey environments: MYGO=new.env(parent=emptyenv()) for (nm in names(res)) MYGO[[nm]] <- res[[nm]] MYENTREZID <- new.env() for (nm in ls(MYGO)) MYENTREZID[[nm]] <- paste("fauxId", nm) #Then we could package them up into a local environments: MYpkg <- new.env(parent=emptyenv()) MYpkg[["MYGO"]] <- MYGO MYpkg[["MYENTREZID"]] <- MYENTREZID #And attach them attach(MYpkg, 2, "package:MY") #At this point we should be able to do with these environments whatever we need to. I have the relevant information here from NCBI for falciparum to make both of these environments (for real). If you send me a personal email, I can arrange to get it to you... Marc ------------------------------ Message: 8 Date: Wed, 07 Nov 2007 20:39:47 -0500 From: "James W. MacDonald" <jmacdon@med.umich.edu> Subject: Re: [BioC] Affymetrix reannotation To: Samuel Wuest <swuest at="" botinst.uzh.ch=""> Cc: Bioconductor at stat.math.ethz.ch Message-ID: <473268E3.5030007 at med.umich.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Samuel, If you just want to ensure the probes in each probeset actually map to the current genome build, then you might consider the MBNI re-mapped cdfs. For the ath1121501 chip there are two you could consider; the ath1atrefseqcdf or ath1attaircdf packages. The probes were first blasted against this version of the genome (1con.01222004, file date is 08/10/2006) -- not sure what that means, as I am not a plant guy. The probes that mapped to a single unique sequence on the genome were then annotated to genes using either TAIR or RefSeq (this is part of the package name above), so you are assured that any probes that are outdated have been removed. More info is available here (note these are version 10): http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF _download.asp#v10 You can get the package(s) in one of two ways. First, you can get them automagically by doing something like: dat <- ReadAffy(filenames=list.celfiles(), cdfname="ath1atrefseqcdf") or you can download/install using biocLite() and then specify in your call to ReadAffy() (or justRMA()/justGCRMA() if you are going that route). Best, Jim Samuel Wuest wrote: > Thanks a lot, > > I am familiar with the ath1121501 package. Now I don?t know whether it > contains informations on the probe-level rather than on the probeset-level > (e.g. whether a designed probe still targets an updated gene model? or which > probe-sets are obsolete and can be considered to be outdated?) > > And: How can I retrieve such information without writing a blast- script to > check every single probe against the most updated cDNA database? > > Thanks for any help on this. > Samuel > > On Tue, 06 Nov 2007 10:31:38 -0800 > Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > >>Samuel Wuest wrote: >> >>>Hi, >>> >>>I trying to assess a modified version of the Affymetrix present/absent >>>call >>>algorithm on my data, which have been generated from two-round amplified >>>RNA >>>hybridized to the Arabidopsis ATH1 GeneChip. >>> >>>I would need some negative control probesets, and thought of probesets >>>that >>>were designed based on wrong gene annotations (similar to what was used in >>>the PANP method from Peter Warren et al.). >>>Therefore, I wondered whether someone does a reannotation of Affy >>>probesets >>>on a regular base? (for example, the version 7 of the Arabidopsis Genome >>>Annotation has been released recently, and some probesets on the AffyChip >>>are most probably not matching any gene model anymore). >>> >>>If yes, where could I find the updated datafiles? Is there anything in the >>>BioC annotation package for the ATH1Chip? >>> >>>Thanks for any help. >>>Best, Sam >>> >>>----------------------------------------------------- >>>Dipl. Bot. Samuel Wust >>>Dep. of Developmental Genetics >>>Institute for Plant Biology >>>University of Zuerich >>>Zollikerstrasse 107 >>>CH - 8008 Z?rich >>>Phone: +41-(0)44 634 82 42 >>>Mobile: + 41 (0)76 501 69 22 >>>Email: swuest at botinst.uzh.ch >>> >>>_______________________________________________ >>>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 >>> >>> >> >>We provide a "standard" annotation package for this chip. You can find >>it here: >> >>http://bioconductor.org/packages/2.1/data/annotation/html/ath1121501 .db.html >> >> >> Marc >> > > > _______________________________________________ > 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 University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ------------------------------ Message: 9 Date: Wed, 07 Nov 2007 21:25:12 -0500 From: Mete Civelek <mete@seas.upenn.edu> Subject: [BioC] GOTERM To: Bioconductor at stat.math.ethz.ch Message-ID: <6.2.0.14.1.20071107211626.049b0750 at mete.mail.seas.upenn.edu> Content-Type: text/plain; charset="us-ascii"; format=flowed Hi All, I have a simple problem that I can't seem to solve. I am using R 2.4.0 on windows. I am trying to get the GO Terms of a list of GO IDs using the following code. The list of GOIDs is in a file labelled SDGO.txt, which is a single column text file with no header. >library(GO) >SDGO<-read.table("SDGO.txt", header=F) >summary(SDGO) V1 GO:0000075: 1 GO:0000375: 1 GO:0000377: 1 GO:0000398: 1 GO:0001503: 1 GO:0001505: 1 (Other) :134 >apply(SDGO, 1, GOTERM) Error in get(x, envir, mode, inherits) : variable "GOTERM" of mode "function" was not found I am sure I am way off in this code since I am a beginner of R and Bioconductor but I will appreciate any help? Best, Mete ------------------------------ Message: 10 Date: Thu, 08 Nov 2007 01:28:43 -0500 From: phguardiol@aol.com Subject: [BioC] Question about a packages not yet in Bioconductor: AffyProbeMiner in R260 under windows To: Bioconductor at stat.math.ethz.ch Message-ID: <8C9EFE7BE8C9965-BA8-39AB at mblk-d19.sysops.aol.com> Content-Type: text/plain Dear colleagues, I m trying to use the AffyProbeMiner packages available from http://gauss.dbb.georgetown.edu/liblab/affyprobeminer/gene.html?that can replace the usual CDF probes and annotation files available in BioC. I m using R 2.6.0 under WinXPPro SP2. I have downloaded the files available on the webpage above in the R library folder. These are gz.rar compressed files and are not recognized in R windows : Packages -> Install packages from local zip files. I have used WinRar to uncompress these files and have copy and paste the?folders (ex: hgu133ageneccds) located in the uncompressed folders (ex: hgu133ageneccds_1.1.0) in the R folder library.?? Then if I type: ?> library(hgu133ageneccds) I obtain the following error: Error in library(hgu133ageneccds) : ? 'hgu133ageneccdscdf' is not a valid package -- installed < 2.0.0? The same is true for all of these files Is it a problem of compatibility with R (too old files ?) ? Should I use a different way to install these packages in R 2.6.0 ? Is there a plan to include these files and their update in BioC metadata ? Thanks for your help and hoping that this request will not be out of scope from this list since it is not a bioconductor package. Philippe Guardiola, MD [[alternative HTML version deleted]] ------------------------------ Message: 11 Date: Wed, 07 Nov 2007 23:21:54 -0800 From: Robert Gentleman <rgentlem@fhcrc.org> Subject: Re: [BioC] GOTERM To: Mete Civelek <mete at="" seas.upenn.edu=""> Cc: Bioconductor at stat.math.ethz.ch Message-ID: <4732B912.7040404 at fhcrc.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed First, your R, and hence your Bioconductor packages are a year out of date, so you should update them. Mete Civelek wrote: > Hi All, > > I have a simple problem that I can't seem to solve. I am using R 2.4.0 on > windows. I am trying to get the GO Terms of a list of GO IDs using the > following code. The list of GOIDs is in a file labelled SDGO.txt, which is > a single column text file with no header. > > >library(GO) > > >SDGO<-read.table("SDGO.txt", header=F) > > >summary(SDGO) > V1 > GO:0000075: 1 > GO:0000375: 1 > GO:0000377: 1 > GO:0000398: 1 > GO:0001503: 1 > GO:0001505: 1 > (Other) :134 > > >apply(SDGO, 1, GOTERM) > Error in get(x, envir, mode, inherits) : variable "GOTERM" of mode > "function" was not found why do you think that is what you should do? something more like mget(SDGO[,1], GOTERM) will be more appropriate or sapply(SDGO[,1], getGOTerm) would be another alternative > > I am sure I am way off in this code since I am a beginner of R and > Bioconductor but I will appreciate any help? > > Best, > > Mete > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org ------------------------------ Message: 12 Date: Wed, 07 Nov 2007 23:27:37 -0800 From: Robert Gentleman <rgentlem@fhcrc.org> Subject: Re: [BioC] Question about a packages not yet in Bioconductor: AffyProbeMiner in R260 under windows To: phguardiol at aol.com Cc: Bioconductor at stat.math.ethz.ch Message-ID: <4732BA69.9060701 at fhcrc.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed It looks like you are using windows and they do not provide packages for windows users. The reason they are not recognized by R is that they won't work. Your options are to 1) install enough tools on your computer to build packages (details can be found on CRAN) 2) use the remapped probe packages that are released through the Bioconductor project for which we do have windows packages I have no idea what the intentions of AffyProbeMiner are, they have never submitted anything, and until they do, it won't even be considered, best wishes Robert phguardiol at aol.com wrote: > Dear colleagues, > > > I m trying to use the AffyProbeMiner packages available from http://gauss.dbb.georgetown.edu/liblab/affyprobeminer/gene.html?that can replace the usual CDF probes and annotation files available in BioC. > > I m using R 2.6.0 under WinXPPro SP2. > I have downloaded the files available on the webpage above in the R library folder. > These are gz.rar compressed files and are not recognized in R windows : Packages -> Install packages from local zip files. > I have used WinRar to uncompress these files and have copy and paste the?folders (ex: hgu133ageneccds) located in the uncompressed folders (ex: hgu133ageneccds_1.1.0) in the R folder library.?? > > Then if I type: > ?> library(hgu133ageneccds) > > I obtain the following error: > Error in library(hgu133ageneccds) : > ? 'hgu133ageneccdscdf' is not a valid package -- installed < 2.0.0? > The same is true for all of these files > > Is it a problem of compatibility with R (too old files ?) ? Should I use a different way to install these packages in R 2.6.0 ? > > > Is there a plan to include these files and their update in BioC metadata ? > > > Thanks for your help > and hoping that this request will not be out of scope from this list since it is not a bioconductor package. > > Philippe Guardiola, MD > > > [[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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org ------------------------------ Message: 13 Date: Thu, 08 Nov 2007 03:33:33 -0500 From: phguardiol@aol.com Subject: [BioC] Re : Question about reannotated Affy annotation files - Question about AffyProbeMiner in R260 under windows To: Bioconductor at stat.math.ethz.ch Message-ID: <8C9EFF92E9FB66A-754-23AD at FRR1-L18.sis.aol.com> Content-Type: text/plain Thanks for these information. Regarding your proposal of??using the remapped probe packages that are released through the Bioconductor project for which we do have windows packages: 1- Are those which are named CustomCDF ? 2- The way to use these??is not clear for me (if these are the one to be used) there are multiple files for a given chip and what they represent,??how they have been built,??and how to use these (for instance??for affy chips using gcrma) is not clearly explained (unless??I have missed something somewhere..?). Could it be possible to obtain a little bit of help on this from the BioC??group....?? Thanks again Philippe Guardiola, MD -----E-mail d'origine----- De : Robert Gentleman <rgentlem at="" fhcrc.org=""> A : phguardiol at aol.com Cc : Bioconductor at stat.math.ethz.ch Envoy?? le : Je 8 Novembre 2007 8:27 Sujet : Re: [BioC] Question about a packages not yet in Bioconductor: AffyProbeMiner in R260 under windows It looks like you are using windows and they do not provide packages for indows users. The reason they are not recognized by R is that they on't work. Your options are to ) install enough tools on your computer to build packages (details can e found on CRAN) ) use the remapped probe packages that are released through the ioconductor project for which we do have windows packages I have no idea what the intentions of AffyProbeMiner are, they have ever submitted anything, and until they do, it won't even be considered, best wishes Robert hguardiol at aol.com wrote: Dear colleagues, I m trying to use the AffyProbeMiner packages available from ttp://gauss.dbb.georgetown.edu/liblab/affyprobeminer/gene.html?that can replace he usual CDF probes and annotation files available in BioC. I m using R 2.6.0 under WinXPPro SP2. I have downloaded the files available on the webpage above in the R library older. These are gz.rar compressed files and are not recognized in R windows : ackages -> Install packages from local zip files. I have used WinRar to uncompress these files and have copy and paste he?folders (ex: hgu133ageneccds) located in the uncompressed folders (ex: gu133ageneccds_1.1.0) in the R folder library.?? Then if I type: ?> library(hgu133ageneccds) I obtain the following error: Error in library(hgu133ageneccds) : ? 'hgu133ageneccdscdf' is not a valid package -- installed < 2.0.0? The same is true for all of these files Is it a problem of compatibility with R (too old files ?) ? Should I use a ifferent way to install these packages in R 2.6.0 ? Is there a plan to include these files and their update in BioC metadata ? Thanks for your help and hoping that this request will not be out of scope from this list since it s not a bioconductor package. Philippe Guardiola, MD [[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 -- obert Gentleman, PhD rogram in Computational Biology ivision of Public Health Sciences red Hutchinson Cancer Research Center 100 Fairview Ave. N, M2-B876 O Box 19024 eattle, Washington 98109-1024 06-667-7700 gentlem at fhcrc.org _______________________________________________ ioconductor mailing list ioconductor at stat.math.ethz.ch ttps://stat.ethz.ch/mailman/listinfo/bioconductor earch the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]] ------------------------------ Message: 14 Date: Thu, 8 Nov 2007 10:56:25 +0200 (EET) From: Jarno Tuimala <jtuimala@csc.fi> Subject: Re: [BioC] Re : Question about reannotated Affy annotation files - Question about AffyProbeMiner in R260 under windows To: phguardiol at aol.com Cc: Bioconductor at stat.math.ethz.ch Message-ID: <pine.lnx.4.62.0711081042300.25104 at="" sampo3.csc.fi=""> Content-Type: text/plain; charset="iso-8859-1" Hi! The methodology of generating these remapped probes packages is described in NAR, and on the the web. See: http://nar.oxfordjournals.org/cgi/content/full/33/20/e175 http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdf readme.htm There is also an example of how to use these package at the end of the readme page. In addition to Bioconductor, you can download the probe packages from: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF _download_v10.asp If you check the list on this site, you'll see that there are several packages for the same chip. These packages are based on different genome features (gene or transcript) or on different databases (Unigene, RefSeq, Entrez Gene, Ensembl, Vega). Note that in order to be able to use GCRMA, you need to install both CDF and probe packages for your chip. Best wishes, Jarno On Thu, 8 Nov 2007 phguardiol at aol.com wrote: > > Thanks for these information. > > Regarding your proposal of??using the remapped probe packages that are released through the > Bioconductor project for which we do have windows packages: > 1- Are those which are named CustomCDF ? > 2- The way to use these??is not clear for me (if these are the one to > be used) there are multiple files for a given chip and what they > represent,??how they have been built,??and how to use these (for > instance??for affy chips using gcrma) is not clearly explained > (unless??I > have missed something somewhere..?). Could it be possible to obtain a > little bit of help on this from the BioC??group....?? > Thanks again > Philippe Guardiola, MD > > > -----E-mail d'origine----- > De : Robert Gentleman <rgentlem at="" fhcrc.org=""> > A : phguardiol at aol.com > Cc : Bioconductor at stat.math.ethz.ch > Envoy?? le : Je 8 Novembre 2007 8:27 > Sujet : Re: [BioC] Question about a packages not yet in Bioconductor: AffyProbeMiner in R260 under windows > > > > It looks like you are using windows and they do not provide packages for > indows users. The reason they are not recognized by R is that they > on't work. > Your options are to > ) install enough tools on your computer to build packages (details can > e found on CRAN) > ) use the remapped probe packages that are released through the > ioconductor project for which we do have windows packages > I have no idea what the intentions of AffyProbeMiner are, they have > ever submitted anything, and until they do, it won't even be considered, > best wishes > Robert > > hguardiol at aol.com wrote: > Dear colleagues, > > > I m trying to use the AffyProbeMiner packages available from > ttp://gauss.dbb.georgetown.edu/liblab/affyprobeminer/gene.html?that can replace > he usual CDF probes and annotation files available in BioC. > > I m using R 2.6.0 under WinXPPro SP2. > I have downloaded the files available on the webpage above in the R library > older. > These are gz.rar compressed files and are not recognized in R windows : > ackages -> Install packages from local zip files. > I have used WinRar to uncompress these files and have copy and paste > he?folders (ex: hgu133ageneccds) located in the uncompressed folders (ex: > gu133ageneccds_1.1.0) in the R folder library.?? > > Then if I type: > ?> library(hgu133ageneccds) > > I obtain the following error: > Error in library(hgu133ageneccds) : > ? 'hgu133ageneccdscdf' is not a valid package -- installed < 2.0.0? > The same is true for all of these files > > Is it a problem of compatibility with R (too old files ?) ? Should I use a > ifferent way to install these packages in R 2.6.0 ? > > > Is there a plan to include these files and their update in BioC metadata ? > > > Thanks for your help > and hoping that this request will not be out of scope from this list since it > s not a bioconductor package. > > Philippe Guardiola, MD > > > [[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 > > -- > obert Gentleman, PhD > rogram in Computational Biology > ivision of Public Health Sciences > red Hutchinson Cancer Research Center > 100 Fairview Ave. N, M2-B876 > O Box 19024 > eattle, Washington 98109-1024 > 06-667-7700 > gentlem at fhcrc.org > _______________________________________________ > ioconductor mailing list > ioconductor at stat.math.ethz.ch > ttps://stat.ethz.ch/mailman/listinfo/bioconductor > earch the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]] > > ---------------------------------------------------------------------- ------- Jarno Tuimala, FT, bioinformatiikan asiantuntija, CSC, PL 405, 02101 Espoo puh.: (09) 457 2226, fax: (09) 457 2302, s-posti: jarno.tuimala at csc.fi CSC on tieteen tietotekniikan keskus, http://www.csc.fi/molbio Jarno Tuimala, PhD, bioinformatics, CSC, P.O.Box 405, FI-02101 Espoo, Finland tel.: +358 9 457 2226, fax: +358 9 457 2302, e-mail: jarno.tuimala at csc.fi CSC is the Finnish IT Center for Science, http://www.csc.fi/molbio ---------------------------------------------------------------------- ------- ------------------------------ Message: 15 Date: Thu, 8 Nov 2007 09:10:50 +0000 From: Alessandro Fazio <fazioalessandro@hotmail.com> Subject: [BioC] optimizazion cluster in Heatmap To: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <blu120-w177771f390b42893b313e4aa8b0 at="" phx.gbl=""> Content-Type: text/plain Hello everybody, I have a problem in doing a cluster with Heatmap. Briefly, I want a cluster with fixed column order and row order depending on the dendrogram produced by the clustering method. BUT, it seems that the row sorting is not optimal, that is genes with similar expression profiles are not group tpgrther but spread. This is the code I used: > mydist <- function(x) cor.dist(x)> myhclust <- function(x) hclust(x, method='average')> heatmap(exprs(exampleSet),Colv=NA, dist=mydist, hclust=myhclust) > sessionInfo()R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale:LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252attached base packages:[1] 'splines' 'tools' 'stats' 'graphics' 'grDevices' 'utils' [7] 'datasets' 'methods' 'base' other attached packages: bioDist GO genefilter survival ALL Rgraphviz geneplotter '1.8.0! ' '1.16.0' '1.14.1' '2.31' '1.4.3' '1.14.1' '1.14.0' lattice annotate Biobase RBGL graph '0.15-4' '1.14.1' '1.14.0' '1.12.0' '1.14.2' ANY idea about what I should do to have a good row sorting? THANK you in advance Regards, Alessandro _________________________________________________________________ [[replacing trailing spam]] [[alternative HTML version deleted]] ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 57, Issue 8 *******************************************