gmane.science.biology.informatics.conductor

Re: RBGL installation issues

Robert Gentleman — 2008-10-07T13:11:54

Hi Iain, The next step is to do what Li Long suggested and take a look at the compiler being used. For our build machines we provide some explicit details (version numbers), http://www.bioconductor.org/checkResults/2.2/bioc-LATEST/lamb1-NodeInfo.html if yours are different that would be the next thing to try and fix best wishes Robert Iain Gallagher wrote:

BioPAX

Michal Kolář — 2008-10-07T13:04:39

Dear all, is anybody able to read BioPAX data into R? And extract, say, metabolic pathways from it? Any suggestion is most appreciated, Cheers, Michal -- ----------------------------------------------------- Michal Kolář Academy of Sciences of the Czech Republic Institute of Molecular Genetics Vídeňská 1083, CZ-14220 Praha, Czech Republic email:kolarmi< at >img.cas.cz _______________________________________________ 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

Re: topGO problem

James W. MacDonald — 2008-10-07T12:58:28

Hi Iain, Iain Gallagher wrote: I certainly hope this isn't how it looks for you! I think the problem occurs because you are not naming all your arguments, and hence are assuming you got the placement of the 'annot' argument correct. Try adding an annot = annotFUN.gene2GO to your call to new() and see if that helps. Best, Jim

Re: revmap question

James W. MacDonald — 2008-10-07T12:51:14

Robert Gentleman wrote: It's a version issue. The hgu133plus2.db package in the current release of BioC has these two probesets mapped, but they no longer appear to be mapped in the upcoming release. Best, Jim

MedlineR

David Enot — 2008-10-07T12:27:26

Dear all, I came across a paper mentionning package called MedlineR. However the original link mentionned in the paper (http://dbsr.duke.edu/pub/MedlineR) does not seem to be working anymore. Because it must been have used by few members of this list, I wonder if someone could point me to an alternative address where I could access this package. Thanks in advance. David ########## David Enot http://sites.google.com/site/enotdavid/ [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Re: revmap question

Robert Gentleman — 2008-10-07T12:33:39

Hi Raffaele, The first looks like a bug, there are some oddities, but mostly it is the rather cute way that R mangles names... > rv = revmap(hgu133plus2ENTREZID) > rv[["1"]] [1] "229819_at" > rv[["100"]] [1] "204639_at" "216705_s_at" > rv[["1000"]] [1] "203440_at" "203441_s_at" and you can then do the looping explicitly, this also solves your second problem. I don't know how "1556117_at" got picked up, that does look wrong and we will need to look in to it. > hgu133plus2ENTREZID$"1556117_at" [1] NA and for "237305_at", I also get an NA :-( best wishes Robert rcaloger wrote:

Re: revmap question

James W. MacDonald — 2008-10-07T12:26:44

Hi Raffaele, rcaloger wrote: Well, not really. This appears to be so because you are unlisting a named list. Since the names have to be unique, R adds an additional integer to the end of duplicate names: > egs <- c("1", "100", "1000") > mget(egs, revmap(hgu133plus2ENTREZID)) $`1` [1] "229819_at" $`100` [1] "1556117_at" "204639_at" "216705_s_at" $`1000` [1] "203440_at" "203441_s_at" "237305_at" Yes. The help for mget is a bit confusing on this point, but you need to use the argument ifnotfound = NA. > egs <- c("1", "100", "1000", "6333") > mget(egs, revmap(hgu133plus2ENTREZID), ifnotfound = NA) $`1` [1] "229819_at" $`100` [1] "1556117_at" "204639_at" "216705_s_at" $`1000` [1] "203440_at" "203441_s_at" "237305_at" $`6333` [1] NA Best, Jim

KEGGgraph ??

Paul Evans — 2008-10-07T12:09:26

Hi, I want to map some KEGG terms on the KEGG hierarchy. I have been looking at keggorth package to do this. Essentially, I would like to map two sets of KEGG pathways (with two different colors) onto the hierarchy. I have done this with GO terms using the GOgraph function in GOstats package. So, how do I simulate a KEGGgraph function? thanks! [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Re: RBGL installation issues

Iain Gallagher — 2008-10-07T08:50:52

Hi Robert & list Sorry for the brevity of my previous message. I am indeed using biocLite. Below is the output from my attempted installation. Running biocinstall version 2.2.11 with R version 2.7.2 Your version of R requires version 2.2 of BioConductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,Â : Â argument 'lib' is missing: using '/home/iain/R/i486-pc-linux-gnu-library/2.7' trying URL 'http://bioconductor.org/packages/2.2/bioc/src/contrib/RBGL_1.16.0.tar.gz' Content type 'application/x-gzip' length 1327240 bytes (1.3 Mb) opened URL ================================================== downloaded 1.3 Mb * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs g++ -I/usr/share/R/includeÂ Â Â Â -IboostInclÂ -fpicÂ -g -O2 -c bbc.cpp -o bbc.o /usr/lib/gcc/i486-linux-gnu/4.1.2/../../../../include/c++/4.1.2/cstdlib:135: error: â::systemâ has not been declared make: *** [bbc.o] Error 1 chmod: cannot access `/home/ia

Re: RBGL installation issues

Li Long — 2008-10-07T08:40:33

RBGL uses C++ templates extensively, previously we encountered various issues using different C++ compilers, even different versions of g++ compilers. Somehow the error msg in the mail is scrambled, I cannot tell what it complains about, but it looks like something related to C++. Probably you could look further into that. Li _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

revmap question

rcaloger — 2008-10-07T08:00:29

Hi, I found very interesting the possibility of using reversing the mapping by revmap in the XXXX.db annotation databases. However, I have two problems: 1) if I use: egs <- c("1", "100", "1000") unlist(mget(egs, revmap(hgu133plus2ENTREZID))) I am getting not only the probesets associated to the three EGs: 1 1001 1002 1003 10001 "229819_at" "1556117_at" "204639_at" "216705_s_at" "203440_at" 10002 10003 "203441_s_at" "237305_at" There is any possibility to avoid this problem? 2) if in the egs vector is present an eg (6333) that is not present in the annotation database I get the following error: egs <- c("1", "100", "1000", "6333") unlist(mget(egs, revmap(hgu133plus2ENTREZID))) Error in .checkKeys(value, Rkeys(x), x< at >ifnotfound) : value for "6333" not found There is any possibility to make a query that simply avoid the unmapped keys? Many thanks Raffaele

Re: Human gene 1.0 st analysis

Mark Robinson — 2008-10-07T06:37:40

Hi Amets. You have a few options for Gene 1.0 ST arrays in and outside of R. Check out the following thread from earlier this year. It captures several options: http://thread.gmane.org/gmane.science.biology.informatics.conductor/18959/focus=18974 ... there you'll find discussion on i) apt tools (outside of R), ii) aroma.affymetrix, iii) oligo ... and another alternative is the 'xps' package. Hope that helps. Mark On 07/10/2008, at 4:47 PM, AMETS SAENZ PEÑA wrote: ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson-WwWqvNR902a3Zbb/xt2tYQ< at >public.gmane.org e: mrobinson-QpO9qclcJEu6c6uEtOJ/EA< at >public.gmane.org p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

export expression set from beadarray

Matthew Vitalone — 2008-10-07T06:20:24

Hi all, How do I get my normalised Illumina data , via bead array, exported into a expression set as a tab delimited .txt file ? I have tried following the notes on the bioconductor website and anything else I can find on the web. I have also looked through previous posts and I have no been able to find the answer. I am not use to beadarray or any command line type analysis. Thanks you so much for you help. Matt Here is my code: (running R2.7.2, and the latest version of beadarray) *library(limma)* *library(beadarray) **BSData = readBeadSummaryData("expset-all.txt", qcFile=NULL, sampleSheet=NULL,sep="\t",skip=8, ProbeID="PROBE_ID", columns = list(exprs = "AVG_Signal", se.exprs="BEAD_STDERR", NoBeads = "Avg_NBEADS", Detection="Detection Pval"), dec=".") **slotNames(BSData) **names(assayData(BSData))* *BSData.log2.qspline = normaliseIllumina(BSData, method="qspline", transform="log2")* *library(convert) eSet = new("ExpressionSet", assayData= exprs(BSData.log2.qspline$AVG_Signal)) *Erro

Human gene 1.0 st analysis

AMETS SAENZ PEÑA — 2008-10-07T05:47:16

Hi, I have previously used R to analyse HG-U133A and B arrays and everything was perfect. I like very much how I could see the PCA plots... However, a colleague of mine has started using arrays "human gene 1.0 st" and we found a problem when we wanted to analyse them. Dr Irizarry told me that this array is not supported in the affy package, and that he thinks oligo package does. But he suggested me to ask in this e-mail. Thank you very much for your help. Waiting for your answer, Best regards, Amets Sáenz Dra. Amets Sáenz Unidad Experimental Hospital Donostia Pº Dr Begiristain s/n San Sebastián 20.014 Tel: 943 00 70 61 FAX: 943 00 70 61 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Re: Protein structure analysis

Diego Diez — 2008-10-07T01:38:49

Hi, not sure if there is a Bioconductor alternative, but you should take a look at Bio3D: http://mccammon.ucsd.edu/~bgrant/bio3d/ D. On Tue, Oct 7, 2008 at 3:14 AM, Paul Evans public.gmane.org> wrote:

Re: RBGL installation issues

Robert Gentleman — 2008-10-07T00:49:48

Hi Iain, Probably the reason for no response is that you have not given sufficient details for anyone to help. Did you use biocLite, and if so, could you show us a bit more than you are? And if you did not - would you please try that, as it is the recommended route. best wishes Robert Iain Gallagher wrote:

Nimblegen Microarray-gene expression analysis usingBiocnductor

Dhiraj Naik — 2008-10-06T21:58:36

Hi, I am postdoc working with genome wide gene expression using Poplar oligonucleotide Nimblgen array. I am beginner in R and bioconductor. I have Nimblgen raw data in .pair file format. I dont know how to use that using Oligo vignette which is available in bioconductor. How to have input file in R format from .pair files? Thanks Dhriaj

topGO problem

Iain Gallagher — 2008-10-06T21:52:00

Hi I'm trying to use topGO to analyse a list of interesting genes generated using the Affy HGU-133plus2 platform but a custom cdf. The gene universe is a list of Ensembl transcript ids. I have annotated these with the BP GO using biomaRt Â go_biological_process_id ensembl_transcript_id 1Â Â Â Â Â Â Â Â Â Â Â Â Â Â GO:0007264Â Â Â Â Â Â ENST00000000233 2Â Â Â Â Â Â Â Â Â Â Â Â Â Â GO:0015031Â Â Â Â Â Â ENST00000000233 3Â Â Â Â Â Â Â Â Â Â Â Â Â Â GO:0016192Â Â Â Â Â Â ENST00000000233 4Â Â Â Â Â Â Â Â Â Â Â Â Â Â GO:0006886Â Â Â Â Â Â ENST00000000233 5Â Â Â Â Â Â Â Â Â Â Â Â Â Â GO:0006810Â Â Â Â Â Â ENST00000000412 6Â Â Â Â Â Â Â Â Â Â Â Â Â Â GO:0006898Â Â Â Â Â Â ENST00000000412 and created a list object for feeding to topGO e.g. List of 13847 Â

RBGL installation issues

Iain Gallagher — 2008-10-06T21:37:04

Hi I posted this a few hours ago on the R-help list but have had no replies. I thought it might be better here. Apologies for cross posting. I'm trying to install the RBGL package in order to install GOstats. However I am getting the following error; can anybody shed some light on what I'm missing? /usr/lib/gcc/i486-linux-gnu/4.1.2/../../../../include/c++/4.1.2/cstdlib:135: error: â::systemâ has not been declared Thanks. Iain R version 2.7.2 (2008-08-25) i486-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] statsÂ Â Â Â graphicsÂ grDevices utilsÂ Â Â Â datasetsÂ methodsÂ Â baseÂ Â Â Â loaded via a namespace (and not attached): [1] tcltk_2.7.2 tools_2.7.2 [[alternative HTML version deleted]] _______________________________________

Re: Overlay Density Plot for FlowSet

Aric Gregson — 2008-10-06T18:38:18

Florian, On Fri, 03 Oct 2008 13:31:57 -0700 Florian Hahne public.gmane.org> wrote: I thought that perhaps the drawing of gates on the densityplot, the lack of contour() working and the fact that none of the gate outlines are ever drawn in xyplot(smooth=F) was due to my environment, so I upgraded. My machine environment is listed below. There was no change in plot results. I then tried on a clean install of R 2.7.2 and the most recent bioconductor packages (as of yesterday) for this version of R on a Mac (sessionInfo not listed) and there was no change in plot behavior. I used the same .RData and .Rhistory files on both machines, before and after the upgrades, if that makes a difference. I must be setting up and adding gates incorrectly or something very odd is going on. I have also noticed that the following example from page 7 of 'filters.pdf' produces different results depending upon which version of the 'filters.pdf' document that I look at. + data = transfor

Protein structure analysis

Paul Evans — 2008-10-06T18:14:48

Hi, I have a set of genes and would like to conduct an analysis to see how much similarity (dis-similarity) there is between the surfaces/structures of the proteins they encode. Which packages should I be looking at? [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor