[BioC] Bioconductor Digest, Vol 73, Issue 8
ramesh aathe
mphil.ramesh at gmail.com
Mon Mar 9 05:00:50 CET 2009
Thanks
With regards,
ramesh
On 3/8/09, bioconductor-request at stat.math.ethz.ch
<bioconductor-request at stat.math.ethz.ch> wrote:
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> 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=en_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_IDENTIFICATION=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
>
>
>
> ------------------------------
>
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>
> End of Bioconductor Digest, Vol 73, Issue 8
> *******************************************
>
--
Thanks and Regards,
Ramesh Athe,
+91-9963126900,
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