Thanks With regards, ramesh On 3/8/09, bioconductor-request at stat.math.ethz.ch <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. Re: Error in HyperGTest with GOHyperGParams class (Pankaj Chopra) > 2. running exonmap package and chimp arrays (Pete Shepard) > 3. Re: biomaRt error (Wolfgang Huber) > 4. reading probe ID file (kuntal worah) > 5. Re: Cloud Plotting? flowViz/Core (Aric Gregson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 07 Mar 2009 06:23:16 -0500 > From: Pankaj Chopra <pchopra at="" ncsu.edu=""> > Subject: Re: [BioC] Error in HyperGTest with GOHyperGParams class > To: Mayte Suarez-Farinas <farinam at="" mail.rockefeller.edu=""> > Cc: bioconductor at stat.math.ethz.ch > Message-ID: <49B25924.3040101 at ncsu.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Would it be possible to get a reproducible example? > > thanks! > > Mayte Suarez-Farinas wrote: > > Hi all, > > I recently updated to R 2.8. I have a list of significant genes and > > want to do hypergeometric test to check for over-representing pathways > > and ontologies. > > For KEGG it works fine but for GO I got the following error: > > > > any help will be appreciated!!! > > > > > > > > >params <- new("KEGGHyperGParams", geneIds = eids, universeGeneIds = > > universe, annotation = lib, pvalueCutoff=1) > > > > > params2 <- new("GOHyperGParams", geneIds = eids, universeGeneIds = > > universe, > > + annotation = lib, ontology = ontology, conditional=cond, > > pvalueCutoff=1) > > > > > > > hyperGTest(params) > > Gene to KEGG test for over-representation > > 116 KEGG ids tested (116 have p < 1) > > Selected gene set size: 139 > > Gene universe size: 3166 > > Annotation package: hgu133a2 > > > > > hyperGTest(params2) > > Error in initialize(value, ...) : > > invalid names for slots of class "GOHyperGResult": pvalues, > > oddsRatios, expectedCounts, catToGeneId > > > > > str(params) > > Formal class 'KEGGHyperGParams' [package "Category"] with 8 slots > > ..@ geneIds : chr [1:394] "3608" "8882" "9948" "163" ... > > ..@ universeGeneIds : chr(0) > > ..@ annotation : chr "hgu133a2" > > ..@ datPkg :Formal class 'AffyDatPkg' [package "Category"] > > with 1 slots > > .. .. ..@ name: chr "hgu133a2" > > ..@ cateogrySubsetIds: NULL > > ..@ categoryName : chr "KEGG" > > ..@ pvalueCutoff : num 1 > > ..@ testDirection : chr "over" > > > > > str(params2) > > Formal class 'GOHyperGParams' [package "Category"] with 10 slots > > ..@ ontology : chr "BP" > > ..@ conditional : logi TRUE > > ..@ geneIds : chr [1:394] "3608" "8882" "9948" "163" ... > > ..@ universeGeneIds : chr(0) > > ..@ annotation : chr "hgu133a2" > > ..@ datPkg :Formal class 'AffyDatPkg' [package "Category"] > > with 1 slots > > .. .. ..@ name: chr "hgu133a2" > > ..@ cateogrySubsetIds: NULL > > ..@ categoryName : chr "GO" > > ..@ pvalueCutoff : num 1 > > ..@ testDirection : chr "over" > > > > > > > > sessionInfo() > > R version 2.8.1 (2008-12-22) > > i386-apple-darwin8.11.1 > > > > locale: > > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] splines tools stats graphics grDevices utils > > datasets methods base > > > > other attached packages: > > [1] statmod_1.3.8 GOstats_2.8.0 > > RBGL_1.18.0 Category_2.8.4 annaffy_1.14.0 > > [6] KEGG.db_2.2.5 GO.db_2.2.5 > > hgu133a2probe_2.3.0 hgu133plus2.db_2.2.5 hgu133a2.db_2.2.5 > > [11] hgu133a2cdf_2.3.0 Harshlight_1.12.0 > > altcdfenvs_2.4.0 hypergraph_1.14.0 graph_1.20.0 > > [16] Biostrings_2.10.16 IRanges_1.0.12 > > makecdfenv_1.20.0 affyio_1.10.1 maCorrPlot_1.12.0 > > [21] lumiHumanIDMapping_1.0.1 lumi_1.8.3 > > mgcv_1.4-1.1 affyQCReport_1.20.0 RColorBrewer_1.0-2 > > [26] affyPLM_1.18.1 preprocessCore_1.4.0 > > simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 > > [31] genefilter_1.22.0 survival_2.34-1 > > affy_1.20.2 lumiHumanAll.db_1.4.0 RSQLite_0.7-1 > > [36] DBI_0.2-4 beadarray_1.10.0 > > sma_0.5.15 hwriter_1.0 geneplotter_1.20.0 > > [41] annotate_1.20.1 xtable_1.5-4 > > AnnotationDbi_1.4.3 lattice_0.17-17 Biobase_2.2.2 > > [46] limma_2.16.4 > > > > loaded via a namespace (and not attached): > > [1] GSEABase_1.4.0 KernSmooth_2.22-22 Matrix_0.999375-21 > > XML_2.1-0 cluster_1.11.11 grid_2.8.1 > > > > _______________________________________________ > > 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: Sat, 7 Mar 2009 04:48:54 -0800 > From: Pete Shepard <peter.shepard at="" gmail.com=""> > Subject: [BioC] running exonmap package and chimp arrays > To: bioconductor at stat.math.ethz.ch > Message-ID: > <5c2c43620903070448m35ecd51qe267a24e54b51f8d at mail.gmail.com> > Content-Type: text/plain > > Dear Bioconductor list, > > I am brand new to Bioconductor and am interested in looking at exon arrays. > I have two questions: > > 1) In the "common workflows" section of the getting started section, it says > that to use the exonmap package I need >=8GB of RAM, I have 2GB. Is there a > way around this? > > 2) Also I would like to look at human exon arrays and chimp/primate exon > arrays. I am wondering if Bioconductor has a list of exon sets and data that > are available to users? > > Thanks > > [[alternative HTML version deleted]] > > > > ------------------------------ > > Message: 3 > Date: Sat, 07 Mar 2009 18:32:31 +0000 > From: Wolfgang Huber <huber at="" ebi.ac.uk=""> > Subject: Re: [BioC] biomaRt error > To: Lakshmanan Iyer <laxvid at="" gmail.com=""> > Cc: bioconductor at stat.math.ethz.ch > Message-ID: <49B2BDBF.6060804 at ebi.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Lakshmanan > > thank you for reporting this! In the future, please send a fully > reproducible example (I cannot tell what the values of your "attributes" > and "snps" variables are). > > Also, can you please try downloading and installing the most recent > version of biomaRt from http://www.bioconductor.org/packages/devel/bioc > and then tell us whether a problem persists. > (For better or worse, the online webservice that biomaRt connects to > updates more frequently, and at different times, than Bioconductor > releases.) > > Thank you > Wolfgang > > ------------------------------------------------ > Wolfgang Huber EMBL http://www.ebi.ac.uk/huber > > > Hi > > I was asked to report this error while running biomaRt. I believe it > > meant report to the list and/or developer! > > So here it goes! > > > >> i2 <- getBM( attributes[c(3:6,16,17,28,62),1], filters="ensembl_gene", values="ENSG00000090861", mart=snps) > > V1 > > 1 Query ERROR: caught BioMart::Exception::Usage: Attribute dbSNP NOT FOUND > > Error in getBM(attributes[c(3:6, 16, 17, 28, 62), 1], filters = > > "ensembl_gene", : > > Number of columns in the query result doesn't equal number of > > attributes in query. This is probably an internal error, please > > report. > > > >> sessionInfo() > > R version 2.8.1 (2008-12-22) > > i486-pc-linux-gnu > > > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID ENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] biomaRt_1.16.0 > > > > loaded via a namespace (and not attached): > > [1] RCurl_0.92-0 tools_2.8.1 XML_1.98-1 > > -Best > > -Lax > > > > _______________________________________________ > > 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: 4 > Date: Sat, 7 Mar 2009 19:05:39 +0100 > From: kuntal worah <worah.kuntal at="" gmail.com=""> > Subject: [BioC] reading probe ID file > To: bioconductor at stat.math.ethz.ch > Message-ID: > <59d315190903071005qe5d875au10114d68626ed96 at mail.gmail.com> > Content-Type: text/plain > > Hi, > > I have output file of Illumina microarray. "Array Content = > HUMANREF-8_V2_11223162_B". > > Data contains the Probe ID and target id. But I am unable to read the file > with probe ID. > > The error it shows. > > ?Annotation columns are not available in the data. > > Duplicated IDs found and were merged! > > Error in se.exprs[selInd.i, ]^2 * (beadNum[selInd.i, ] - 1) : > > non-conformable arrays > > In addition: Warning message: > > In lumiR("probe1.txt", lib.mapping = "lumiHumanIDMapping") : > > The raw data should not be normalized in BeadStudio. ? > > Any suggestion for this problem?? > > [[alternative HTML version deleted]] > > > > ------------------------------ > > Message: 5 > Date: Sat, 07 Mar 2009 12:27:40 -0800 > From: Aric Gregson <a.gregson at="" ucla.edu=""> > Subject: Re: [BioC] Cloud Plotting? flowViz/Core > To: Florian Hahne <fhahne at="" fhcrc.org="">, a.gregson at ucla.edu > Cc: bioconductor at stat.math.ethz.ch > Message-ID: <ee7195cd13dfc52c6afe1ba1 at="" powermac1-2.local=""> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Florian, > > --On March 6, 2009 2:02:30 PM -0800 Florian Hahne <fhahne at="" fhcrc.org=""> wrote: > > >> There does not appear to be any implementation of the corresponding > >> cloud plot from lattice in flowViz, is that correct? Would it be > >> possible or is it planned to implement it? > >> > > at the moment there are no concrete plans of doing so. However, you are > > invited to try an implementation yourself. All that needs to be done is > > to write an S4 method for flowFrames and flowSets, and it might be as > > simple as extracting the data and faking the necessary formula to plot > > the right parameters. However, I expect this to be very slow because > > typical flow data sets are too big to efficiently plot individual points, > > and a 3D density representation might be more useful. > > Yes, I actually meant to say 3D cloud. I don't think that cloud itself > would be very useful. > > Aric > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > End of Bioconductor Digest, Vol 73, Issue 8 > ******************************************* > -- Thanks and Regards, Ramesh Athe, +91-9963126900,