Bioconductor Digest, Vol 73, Issue 8
0
0
Entering edit mode
ramesh aathe ▴ 10
@ramesh-aathe-3326
Last seen 10.3 years ago
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,
Microarray Annotation GO hgu133plus2 probe biomaRt flowViz exonmap Microarray Annotation • 1.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 552 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6