Nonspecific filtering on Human Gene ST 1.0 Arrays
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@javier-perez-florido-3121
Last seen 6.7 years ago
Dear list, I've tried to use the nsFilter function from genefilter package to perform nonspecific filtering on a Human Gene ST 1.0 dataset. The expression set has the hugene10sttranscriptcluster.db annotation package, but when nsFilter is applied: nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without EntrezGene IDs, etc Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : "hugene10sttranscriptcluster.db_dbconn" cannot be found Maybe nsFilter is not built for this kind of microarrays, although varFilter,from the same package, works, because it makes use of the expression values only. I've made some search on Google, but no success. I can write a function that removes the different control genes in Human Gene (AFFX, spike, neg_control,pos_control,etc) and those without EntrezGene ID, but wanted to know if there is a function that handle this for this kind of microarrays. Thanks, Javier sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Matrix_0.999375-31 lattice_0.17-26 [3] ALL_1.4.7 genefilter_1.28.0 [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 [7] KEGG.db_2.3.5 hugene10sttranscriptcluster.db_4.0.1 [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 [11] DBI_0.2-4 oligo_1.10.0 [13] preprocessCore_1.8.0 oligoClasses_1.8.0 [15] GSEABase_1.8.0 graph_1.24.0 [17] annotate_1.24.0 AnnotationDbi_1.8.0 [19] Biobase_2.6.0 loaded via a namespace (and not attached): [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 XML_2.6-0 xtable_1.5-5 >
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@vincent-j-carey-jr-4
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@vincent-j-carey-jr-4
Last seen 10 weeks ago
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2009/11/24 Javier Pérez Florido <jpflorido@gmail.com> > Dear list, > I've tried to use the nsFilter function from genefilter package to perform > nonspecific filtering on a Human Gene ST 1.0 dataset. > The expression set has the hugene10sttranscriptcluster.db annotation > package, but when nsFilter is applied: > > nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without > EntrezGene IDs, etc > Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : > "hugene10sttranscriptcluster.db_dbconn" cannot be found > The reason for this error is that the defaults include things like require.entrez=TRUE, which would require an ability to map probes to entrez genes. if you set require.entrez and remove.dupEntrez to FALSE, it should work. > > Maybe nsFilter is not built for this kind of microarrays, although > varFilter,from the same package, works, because it makes use of the > expression values only. > > I've made some search on Google, but no success. I can write a function > that removes the different control genes in Human Gene (AFFX, spike, > neg_control,pos_control,etc) and those without EntrezGene ID, but wanted to > know if there is a function that handle this for this kind of microarrays. > > Thanks, > Javier > > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] > LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] > LC_TIME=Spanish_Spain.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] Matrix_0.999375-31 lattice_0.17-26 > [3] ALL_1.4.7 genefilter_1.28.0 > [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 > [7] KEGG.db_2.3.5 > hugene10sttranscriptcluster.db_4.0.1 > [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 > [11] DBI_0.2-4 oligo_1.10.0 > [13] preprocessCore_1.8.0 oligoClasses_1.8.0 > [15] GSEABase_1.8.0 graph_1.24.0 > [17] annotate_1.24.0 AnnotationDbi_1.8.0 > [19] Biobase_2.6.0 > loaded via a namespace (and not attached): > [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 grid_2.10.0 > [5] IRanges_1.4.0 RBGL_1.20.0 splines_2.10.0 survival_2.35-7 > [9] tools_2.10.0 XML_2.6-0 xtable_1.5-5 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 10 hours ago
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Hi Javier, Javier P?rez Florido wrote: > Dear list, > I've tried to use the nsFilter function from genefilter package to > perform nonspecific filtering on a Human Gene ST 1.0 dataset. > The expression set has the hugene10sttranscriptcluster.db annotation > package, but when nsFilter is applied: > > nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without > EntrezGene IDs, etc > Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : > "hugene10sttranscriptcluster.db_dbconn" cannot be found annotation(subEset) <- "hugene10sttranscriptcluster" Should do the trick. Best, Jim > > Maybe nsFilter is not built for this kind of microarrays, although > varFilter,from the same package, works, because it makes use of the > expression values only. > > I've made some search on Google, but no success. I can write a function > that removes the different control genes in Human Gene (AFFX, spike, > neg_control,pos_control,etc) and those without EntrezGene ID, but wanted > to know if there is a function that handle this for this kind of > microarrays. > > Thanks, > Javier > > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] > LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] > LC_TIME=Spanish_Spain.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] Matrix_0.999375-31 > lattice_0.17-26 [3] > ALL_1.4.7 genefilter_1.28.0 > [5] pd.hugene.1.0.st.v1_3.0.0 > Category_2.12.0 [7] > KEGG.db_2.3.5 hugene10sttranscriptcluster.db_4.0.1 > [9] org.Hs.eg.db_2.3.6 > RSQLite_0.7-3 [11] > DBI_0.2-4 oligo_1.10.0 > [13] preprocessCore_1.8.0 > oligoClasses_1.8.0 [15] > GSEABase_1.8.0 graph_1.24.0 > [17] annotate_1.24.0 > AnnotationDbi_1.8.0 [19] Biobase_2.6.0 > loaded via a namespace (and not attached): > [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 > grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 > splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 > XML_2.6-0 xtable_1.5-5 > > > _______________________________________________ > 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, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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@martin-morgan-1513
Last seen 4 months ago
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"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Hi Javier, > > Javier P?rez Florido wrote: >> Dear list, >> I've tried to use the nsFilter function from genefilter package to >> perform nonspecific filtering on a Human Gene ST 1.0 dataset. >> The expression set has the hugene10sttranscriptcluster.db annotation >> package, but when nsFilter is applied: >> nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without >> EntrezGene IDs, etc >> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >> "hugene10sttranscriptcluster.db_dbconn" cannot be found > > annotation(subEset) <- "hugene10sttranscriptcluster" genefilter 1.28.1 should work for both "hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster". Martin > Should do the trick. > > Best, > > Jim > > >> Maybe nsFilter is not built for this kind of microarrays, although >> varFilter,from the same package, works, because it makes use of the >> expression values only. >> I've made some search on Google, but no success. I can write a >> function that removes the different control genes in Human Gene >> (AFFX, spike, neg_control,pos_control,etc) and those without >> EntrezGene ID, but wanted to know if there is a function that handle >> this for this kind of microarrays. >> Thanks, >> Javier >> sessionInfo() >> R version 2.10.0 (2009-10-26) >> i386-pc-mingw32 >> locale: >> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] >> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] >> LC_TIME=Spanish_Spain.1252 attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> other attached packages: >> [1] Matrix_0.999375-31 lattice_0.17-26 >> [3] ALL_1.4.7 genefilter_1.28.0 >> [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 >> [7] KEGG.db_2.3.5 >> hugene10sttranscriptcluster.db_4.0.1 >> [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >> [11] DBI_0.2-4 oligo_1.10.0 >> [13] preprocessCore_1.8.0 oligoClasses_1.8.0 >> [15] GSEABase_1.8.0 graph_1.24.0 >> [17] annotate_1.24.0 AnnotationDbi_1.8.0 >> [19] Biobase_2.6.0 loaded via a namespace (and >> not attached): >> [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 >> grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 >> splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 XML_2.6-0 >> xtable_1.5-5 > >> _______________________________________________ >> 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Martin Morgan escribi?: > "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > > >> Hi Javier, >> >> Javier P?rez Florido wrote: >> >>> Dear list, >>> I've tried to use the nsFilter function from genefilter package to >>> perform nonspecific filtering on a Human Gene ST 1.0 dataset. >>> The expression set has the hugene10sttranscriptcluster.db annotation >>> package, but when nsFilter is applied: >>> nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without >>> EntrezGene IDs, etc >>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>> >> annotation(subEset) <- "hugene10sttranscriptcluster" >> > > genefilter 1.28.1 should work for both > "hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster". > I've checked that it only works when annotation(subEset) <- "hugene10sttranscriptcluster" Javier > Martin > > >> Should do the trick. >> >> Best, >> >> Jim >> >> >> >>> Maybe nsFilter is not built for this kind of microarrays, although >>> varFilter,from the same package, works, because it makes use of the >>> expression values only. >>> I've made some search on Google, but no success. I can write a >>> function that removes the different control genes in Human Gene >>> (AFFX, spike, neg_control,pos_control,etc) and those without >>> EntrezGene ID, but wanted to know if there is a function that handle >>> this for this kind of microarrays. >>> Thanks, >>> Javier >>> sessionInfo() >>> R version 2.10.0 (2009-10-26) >>> i386-pc-mingw32 >>> locale: >>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] >>> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] >>> LC_TIME=Spanish_Spain.1252 attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> other attached packages: >>> [1] Matrix_0.999375-31 lattice_0.17-26 >>> [3] ALL_1.4.7 genefilter_1.28.0 >>> [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 >>> [7] KEGG.db_2.3.5 >>> hugene10sttranscriptcluster.db_4.0.1 >>> [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >>> [11] DBI_0.2-4 oligo_1.10.0 >>> [13] preprocessCore_1.8.0 oligoClasses_1.8.0 >>> [15] GSEABase_1.8.0 graph_1.24.0 >>> [17] annotate_1.24.0 AnnotationDbi_1.8.0 >>> [19] Biobase_2.6.0 loaded via a namespace (and >>> not attached): >>> [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 >>> grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 >>> splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 XML_2.6-0 >>> xtable_1.5-5 > >>> _______________________________________________ >>> 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 >>> > >
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Javier P?rez Florido wrote: > Martin Morgan escribi?: >> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: >> >> >>> Hi Javier, >>> >>> Javier P?rez Florido wrote: >>> >>>> Dear list, >>>> I've tried to use the nsFilter function from genefilter package to >>>> perform nonspecific filtering on a Human Gene ST 1.0 dataset. >>>> The expression set has the hugene10sttranscriptcluster.db annotation >>>> package, but when nsFilter is applied: >>>> nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without >>>> EntrezGene IDs, etc >>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>> >>> annotation(subEset) <- "hugene10sttranscriptcluster" >>> >> >> genefilter 1.28.1 should work for both >> "hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster". >> > I've checked that it only works when > > annotation(subEset) <- "hugene10sttranscriptcluster" Can you be more specific? The previous error was >>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found if you see the same message then can you confirm that you have genefilter 1.28.1 installed? If there is a different error then can you please provide me with that? I do not have a 'real' hugene eset with which to work. Martin > > Javier > > >> Martin >> >> >>> Should do the trick. >>> >>> Best, >>> >>> Jim >>> >>> >>> >>>> Maybe nsFilter is not built for this kind of microarrays, although >>>> varFilter,from the same package, works, because it makes use of the >>>> expression values only. >>>> I've made some search on Google, but no success. I can write a >>>> function that removes the different control genes in Human Gene >>>> (AFFX, spike, neg_control,pos_control,etc) and those without >>>> EntrezGene ID, but wanted to know if there is a function that handle >>>> this for this kind of microarrays. >>>> Thanks, >>>> Javier >>>> sessionInfo() >>>> R version 2.10.0 (2009-10-26) >>>> i386-pc-mingw32 >>>> locale: >>>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] >>>> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] >>>> LC_TIME=Spanish_Spain.1252 attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> other attached packages: >>>> [1] Matrix_0.999375-31 lattice_0.17-26 >>>> [3] ALL_1.4.7 genefilter_1.28.0 >>>> [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 >>>> [7] KEGG.db_2.3.5 >>>> hugene10sttranscriptcluster.db_4.0.1 >>>> [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >>>> [11] DBI_0.2-4 oligo_1.10.0 >>>> [13] preprocessCore_1.8.0 oligoClasses_1.8.0 >>>> [15] GSEABase_1.8.0 graph_1.24.0 >>>> [17] annotate_1.24.0 AnnotationDbi_1.8.0 >>>> [19] Biobase_2.6.0 loaded via a namespace (and >>>> not attached): >>>> [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 >>>> grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 >>>> splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 XML_2.6-0 >>>> xtable_1.5-5 > >>>> _______________________________________________ >>>> 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 >>>> >> >> > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Martin Morgan escribi?: > Javier P?rez Florido wrote: > >> Martin Morgan escribi?: >> >>> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: >>> >>> >>> >>>> Hi Javier, >>>> >>>> Javier P?rez Florido wrote: >>>> >>>> >>>>> Dear list, >>>>> I've tried to use the nsFilter function from genefilter package to >>>>> perform nonspecific filtering on a Human Gene ST 1.0 dataset. >>>>> The expression set has the hugene10sttranscriptcluster.db annotation >>>>> package, but when nsFilter is applied: >>>>> nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without >>>>> EntrezGene IDs, etc >>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>>> >>>>> >>>> annotation(subEset) <- "hugene10sttranscriptcluster" >>>> >>>> >>> genefilter 1.28.1 should work for both >>> "hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster". >>> >>> >> I've checked that it only works when >> >> annotation(subEset) <- "hugene10sttranscriptcluster" >> > > Can you be more specific? The previous error was > > >>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>>> > > if you see the same message then can you confirm that you have > genefilter 1.28.1 installed? If there is a different error then can you > please provide me with that? I do not have a 'real' hugene eset with > which to work. > > Martin > Dear Martin, I've updated genefilter from version 1.28.0 to version 1.28.1. When I'm trying to use genefilter annotation(OligoEset) <- "hugene10sttranscriptcluster.db" OligoEset<-nsFilter(OligoEset, require.entrez=TRUE,require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE, feature.exclude="petete")$eset Error in get(paste(data, centID, sep = "")) : object 'hugene10sttranscriptcluster.dbENTREZID' not found However, if annotation(OligoEset) <- "hugene10sttranscriptcluster" nsFilter works well. Hope this helps, Javier R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.hugene.1.0.st.v1_3.0.0 oligo_1.10.0 preprocessCore_1.8.0 [4] oligoClasses_1.8.0 genefilter_1.28.1 GOstats_2.12.0 [7] graph_1.24.0 Category_2.12.0 limma_3.2.1 [10] hugene10sttranscriptcluster.db_4.0.1 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 [13] DBI_0.2-4 AnnotationDbi_1.8.0 vsn_3.14.0 [16] Biobase_2.6.0 loaded via a namespace (and not attached): [1] affxparser_1.18.0 affy_1.24.0 affyio_1.14.0 annotate_1.24.0 Biostrings_2.14.0 GO.db_2.3.5 grid_2.10.0 [8] GSEABase_1.8.0 IRanges_1.4.0 lattice_0.17-26 RBGL_1.20.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 [15] XML_2.6-0 xtable_1.5-5 > >> Javier >> >> >> >>> Martin >>> >>> >>> >>>> Should do the trick. >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>> >>>>> Maybe nsFilter is not built for this kind of microarrays, although >>>>> varFilter,from the same package, works, because it makes use of the >>>>> expression values only. >>>>> I've made some search on Google, but no success. I can write a >>>>> function that removes the different control genes in Human Gene >>>>> (AFFX, spike, neg_control,pos_control,etc) and those without >>>>> EntrezGene ID, but wanted to know if there is a function that handle >>>>> this for this kind of microarrays. >>>>> Thanks, >>>>> Javier >>>>> sessionInfo() >>>>> R version 2.10.0 (2009-10-26) >>>>> i386-pc-mingw32 >>>>> locale: >>>>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] >>>>> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] >>>>> LC_TIME=Spanish_Spain.1252 attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> other attached packages: >>>>> [1] Matrix_0.999375-31 lattice_0.17-26 >>>>> [3] ALL_1.4.7 genefilter_1.28.0 >>>>> [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 >>>>> [7] KEGG.db_2.3.5 >>>>> hugene10sttranscriptcluster.db_4.0.1 >>>>> [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >>>>> [11] DBI_0.2-4 oligo_1.10.0 >>>>> [13] preprocessCore_1.8.0 oligoClasses_1.8.0 >>>>> [15] GSEABase_1.8.0 graph_1.24.0 >>>>> [17] annotate_1.24.0 AnnotationDbi_1.8.0 >>>>> [19] Biobase_2.6.0 loaded via a namespace (and >>>>> not attached): >>>>> [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 >>>>> grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 >>>>> splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 XML_2.6-0 >>>>> xtable_1.5-5 > >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>> >>> > > >
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Hi Javier -- Javier P?rez Florido wrote: > Martin Morgan escribi?: >> Javier P?rez Florido wrote: >> >>> Martin Morgan escribi?: >>> >>>> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: >>>> >>>> >>>> >>>>> Hi Javier, >>>>> >>>>> Javier P?rez Florido wrote: >>>>> >>>>>> Dear list, >>>>>> I've tried to use the nsFilter function from genefilter package to >>>>>> perform nonspecific filtering on a Human Gene ST 1.0 dataset. >>>>>> The expression set has the hugene10sttranscriptcluster.db annotation >>>>>> package, but when nsFilter is applied: >>>>>> nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without >>>>>> EntrezGene IDs, etc >>>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>>>> >>>>> annotation(subEset) <- "hugene10sttranscriptcluster" >>>>> >>>> genefilter 1.28.1 should work for both >>>> "hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster". >>>> >>> I've checked that it only works when >>> >>> annotation(subEset) <- "hugene10sttranscriptcluster" >>> >> >> Can you be more specific? The previous error was >> >> >>>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>>>> >> >> if you see the same message then can you confirm that you have >> genefilter 1.28.1 installed? If there is a different error then can you >> please provide me with that? I do not have a 'real' hugene eset with >> which to work. >> >> Martin >> > Dear Martin, > I've updated genefilter from version 1.28.0 to version 1.28.1. When I'm > trying to use genefilter > > annotation(OligoEset) <- "hugene10sttranscriptcluster.db" > OligoEset<-nsFilter(OligoEset, require.entrez=TRUE,require.GOBP=TRUE, > remove.dupEntrez=TRUE, > var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE, > feature.exclude="petete")$eset > Error in get(paste(data, centID, sep = "")) : > object 'hugene10sttranscriptcluster.dbENTREZID' not found > > However, if > annotation(OligoEset) <- "hugene10sttranscriptcluster" > > nsFilter works well. Thanks for this. As Robert mentions, the intention is that nsFilter should work whether or not the '.db' extension is present. Changes in the last development cycle introduced bugs where this was not the case. 1.28.1 addressed this in one location, this is a second; version 1.28.2 should fix this when it becomes available, probably after noon (Seattle time) tomorrow. Martin > > Hope this helps, > Javier > > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 > LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] > LC_TIME=Spanish_Spain.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] pd.hugene.1.0.st.v1_3.0.0 > oligo_1.10.0 preprocessCore_1.8.0 > [4] oligoClasses_1.8.0 > genefilter_1.28.1 GOstats_2.12.0 > [7] graph_1.24.0 > Category_2.12.0 limma_3.2.1 > [10] hugene10sttranscriptcluster.db_4.0.1 > org.Hs.eg.db_2.3.6 RSQLite_0.7-3 > [13] DBI_0.2-4 > AnnotationDbi_1.8.0 vsn_3.14.0 > [16] Biobase_2.6.0 > loaded via a namespace (and not attached): > [1] affxparser_1.18.0 affy_1.24.0 affyio_1.14.0 > annotate_1.24.0 Biostrings_2.14.0 GO.db_2.3.5 grid_2.10.0 > [8] GSEABase_1.8.0 IRanges_1.4.0 lattice_0.17-26 > RBGL_1.20.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 > [15] XML_2.6-0 xtable_1.5-5 >> >>> Javier >>> >>> >>> >>>> Martin >>>> >>>> >>>> >>>>> Should do the trick. >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>> >>>>>> Maybe nsFilter is not built for this kind of microarrays, although >>>>>> varFilter,from the same package, works, because it makes use of the >>>>>> expression values only. >>>>>> I've made some search on Google, but no success. I can write a >>>>>> function that removes the different control genes in Human Gene >>>>>> (AFFX, spike, neg_control,pos_control,etc) and those without >>>>>> EntrezGene ID, but wanted to know if there is a function that handle >>>>>> this for this kind of microarrays. >>>>>> Thanks, >>>>>> Javier >>>>>> sessionInfo() >>>>>> R version 2.10.0 (2009-10-26) >>>>>> i386-pc-mingw32 >>>>>> locale: >>>>>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] >>>>>> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] >>>>>> LC_TIME=Spanish_Spain.1252 attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> other attached packages: >>>>>> [1] Matrix_0.999375-31 lattice_0.17-26 >>>>>> [3] ALL_1.4.7 genefilter_1.28.0 >>>>>> [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 >>>>>> [7] KEGG.db_2.3.5 >>>>>> hugene10sttranscriptcluster.db_4.0.1 >>>>>> [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >>>>>> [11] DBI_0.2-4 oligo_1.10.0 >>>>>> [13] preprocessCore_1.8.0 oligoClasses_1.8.0 >>>>>> [15] GSEABase_1.8.0 graph_1.24.0 >>>>>> [17] annotate_1.24.0 AnnotationDbi_1.8.0 >>>>>> [19] Biobase_2.6.0 loaded via a namespace (and >>>>>> not attached): >>>>>> [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 >>>>>> grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 >>>>>> splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 XML_2.6-0 >>>>>> xtable_1.5-5 > >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>> >> >> >> > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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This is possibly due to my email about one week ago when I suggested that: annotation(OligoEset) <- "hugene10sttranscriptcluster.db" would suffice. But apparently the ".db" bit isn't required. b On Nov 27, 2009, at 1:51 PM, Javier P?rez Florido wrote: > Martin Morgan escribi?: >> Javier P?rez Florido wrote: >> >>> Martin Morgan escribi?: >>> >>>> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: >>>> >>>> >>>> >>>>> Hi Javier, >>>>> >>>>> Javier P?rez Florido wrote: >>>>> >>>>> >>>>>> Dear list, >>>>>> I've tried to use the nsFilter function from genefilter package >>>>>> to >>>>>> perform nonspecific filtering on a Human Gene ST 1.0 dataset. >>>>>> The expression set has the hugene10sttranscriptcluster.db >>>>>> annotation >>>>>> package, but when nsFilter is applied: >>>>>> nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those >>>>>> without >>>>>> EntrezGene IDs, etc >>>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>>>> >>>>>> >>>>> annotation(subEset) <- "hugene10sttranscriptcluster" >>>>> >>>>> >>>> genefilter 1.28.1 should work for both >>>> "hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster". >>>> >>>> >>> I've checked that it only works when >>> >>> annotation(subEset) <- "hugene10sttranscriptcluster" >>> >> >> Can you be more specific? The previous error was >> >> >>>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>>>> >> >> if you see the same message then can you confirm that you have >> genefilter 1.28.1 installed? If there is a different error then can >> you >> please provide me with that? I do not have a 'real' hugene eset with >> which to work. >> >> Martin >> > Dear Martin, > I've updated genefilter from version 1.28.0 to version 1.28.1. When > I'm > trying to use genefilter > > annotation(OligoEset) <- "hugene10sttranscriptcluster.db" > OligoEset<-nsFilter(OligoEset, require.entrez=TRUE,require.GOBP=TRUE, > remove.dupEntrez=TRUE, > var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE, > feature.exclude="petete")$eset > Error in get(paste(data, centID, sep = "")) : > object 'hugene10sttranscriptcluster.dbENTREZID' not found > > However, if > annotation(OligoEset) <- "hugene10sttranscriptcluster" > > nsFilter works well. > > Hope this helps, > Javier > > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 > LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C > [5] LC_TIME=Spanish_Spain.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.hugene.1.0.st.v1_3.0.0 > oligo_1.10.0 preprocessCore_1.8.0 > [4] oligoClasses_1.8.0 > genefilter_1.28.1 GOstats_2.12.0 > [7] graph_1.24.0 > Category_2.12.0 limma_3.2.1 > [10] hugene10sttranscriptcluster.db_4.0.1 > org.Hs.eg.db_2.3.6 RSQLite_0.7-3 > [13] DBI_0.2-4 > AnnotationDbi_1.8.0 vsn_3.14.0 > [16] Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.18.0 affy_1.24.0 affyio_1.14.0 > annotate_1.24.0 Biostrings_2.14.0 GO.db_2.3.5 grid_2.10.0 > [8] GSEABase_1.8.0 IRanges_1.4.0 lattice_0.17-26 > RBGL_1.20.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 > [15] XML_2.6-0 xtable_1.5-5 >> >>> Javier >>> >>> >>> >>>> Martin >>>> >>>> >>>> >>>>> Should do the trick. >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>> >>>>> >>>>>> Maybe nsFilter is not built for this kind of microarrays, >>>>>> although >>>>>> varFilter,from the same package, works, because it makes use of >>>>>> the >>>>>> expression values only. >>>>>> I've made some search on Google, but no success. I can write a >>>>>> function that removes the different control genes in Human Gene >>>>>> (AFFX, spike, neg_control,pos_control,etc) and those without >>>>>> EntrezGene ID, but wanted to know if there is a function that >>>>>> handle >>>>>> this for this kind of microarrays. >>>>>> Thanks, >>>>>> Javier >>>>>> sessionInfo() >>>>>> R version 2.10.0 (2009-10-26) >>>>>> i386-pc-mingw32 >>>>>> locale: >>>>>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 >>>>>> [3] >>>>>> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] >>>>>> LC_TIME=Spanish_Spain.1252 attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods >>>>>> base >>>>>> other attached packages: >>>>>> [1] Matrix_0.999375-31 lattice_0.17-26 >>>>>> [3] ALL_1.4.7 genefilter_1.28.0 >>>>>> [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 >>>>>> [7] KEGG.db_2.3.5 >>>>>> hugene10sttranscriptcluster.db_4.0.1 >>>>>> [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >>>>>> [11] DBI_0.2-4 oligo_1.10.0 >>>>>> [13] preprocessCore_1.8.0 oligoClasses_1.8.0 >>>>>> [15] GSEABase_1.8.0 graph_1.24.0 >>>>>> [17] annotate_1.24.0 AnnotationDbi_1.8.0 >>>>>> [19] Biobase_2.6.0 loaded via a namespace >>>>>> (and >>>>>> not attached): >>>>>> [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 >>>>>> grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 >>>>>> splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 XML_2.6-0 >>>>>> xtable_1.5-5 > >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>>>> >>>> >>>> >> >> >> > > _______________________________________________ > 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
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Hi, Benilton Carvalho wrote: > This is possibly due to my email about one week ago when I suggested that: > > annotation(OligoEset) <- "hugene10sttranscriptcluster.db" > > would suffice. But apparently the ".db" bit isn't required. it should not be. It is essentially conveying an implementation detail (that this annotation package is stored as a database), clearly other implementations (like our old environment based one should also work, if one wanted to use them). So my preference is that the .db not be required. best wishes Robert > > b > > On Nov 27, 2009, at 1:51 PM, Javier P?rez Florido wrote: > >> Martin Morgan escribi?: >>> Javier P?rez Florido wrote: >>> >>>> Martin Morgan escribi?: >>>> >>>>> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: >>>>> >>>>> >>>>> >>>>>> Hi Javier, >>>>>> >>>>>> Javier P?rez Florido wrote: >>>>>> >>>>>> >>>>>>> Dear list, >>>>>>> I've tried to use the nsFilter function from genefilter package to >>>>>>> perform nonspecific filtering on a Human Gene ST 1.0 dataset. >>>>>>> The expression set has the hugene10sttranscriptcluster.db annotation >>>>>>> package, but when nsFilter is applied: >>>>>>> nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without >>>>>>> EntrezGene IDs, etc >>>>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>>>>> >>>>>>> >>>>>> annotation(subEset) <- "hugene10sttranscriptcluster" >>>>>> >>>>>> >>>>> genefilter 1.28.1 should work for both >>>>> "hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster". >>>>> >>>>> >>>> I've checked that it only works when >>>> >>>> annotation(subEset) <- "hugene10sttranscriptcluster" >>>> >>> >>> Can you be more specific? The previous error was >>> >>> >>>>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>>>>> >>> >>> if you see the same message then can you confirm that you have >>> genefilter 1.28.1 installed? If there is a different error then can you >>> please provide me with that? I do not have a 'real' hugene eset with >>> which to work. >>> >>> Martin >>> >> Dear Martin, >> I've updated genefilter from version 1.28.0 to version 1.28.1. When I'm >> trying to use genefilter >> >> annotation(OligoEset) <- "hugene10sttranscriptcluster.db" >> OligoEset<-nsFilter(OligoEset, require.entrez=TRUE,require.GOBP=TRUE, >> remove.dupEntrez=TRUE, >> var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE, >> feature.exclude="petete")$eset >> Error in get(paste(data, centID, sep = "")) : >> object 'hugene10sttranscriptcluster.dbENTREZID' not found >> >> However, if >> annotation(OligoEset) <- "hugene10sttranscriptcluster" >> >> nsFilter works well. >> >> Hope this helps, >> Javier >> >> R version 2.10.0 (2009-10-26) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 >> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C >> [5] LC_TIME=Spanish_Spain.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] pd.hugene.1.0.st.v1_3.0.0 >> oligo_1.10.0 preprocessCore_1.8.0 >> [4] oligoClasses_1.8.0 >> genefilter_1.28.1 GOstats_2.12.0 >> [7] graph_1.24.0 >> Category_2.12.0 limma_3.2.1 >> [10] hugene10sttranscriptcluster.db_4.0.1 >> org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >> [13] DBI_0.2-4 >> AnnotationDbi_1.8.0 vsn_3.14.0 >> [16] Biobase_2.6.0 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.18.0 affy_1.24.0 affyio_1.14.0 >> annotate_1.24.0 Biostrings_2.14.0 GO.db_2.3.5 grid_2.10.0 >> [8] GSEABase_1.8.0 IRanges_1.4.0 lattice_0.17-26 >> RBGL_1.20.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 >> [15] XML_2.6-0 xtable_1.5-5 >>> >>>> Javier >>>> >>>> >>>> >>>>> Martin >>>>> >>>>> >>>>> >>>>>> Should do the trick. >>>>>> >>>>>> Best, >>>>>> >>>>>> Jim >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Maybe nsFilter is not built for this kind of microarrays, although >>>>>>> varFilter,from the same package, works, because it makes use of the >>>>>>> expression values only. >>>>>>> I've made some search on Google, but no success. I can write a >>>>>>> function that removes the different control genes in Human Gene >>>>>>> (AFFX, spike, neg_control,pos_control,etc) and those without >>>>>>> EntrezGene ID, but wanted to know if there is a function that handle >>>>>>> this for this kind of microarrays. >>>>>>> Thanks, >>>>>>> Javier >>>>>>> sessionInfo() >>>>>>> R version 2.10.0 (2009-10-26) >>>>>>> i386-pc-mingw32 >>>>>>> locale: >>>>>>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] >>>>>>> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] >>>>>>> LC_TIME=Spanish_Spain.1252 attached base packages: >>>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>>> other attached packages: >>>>>>> [1] Matrix_0.999375-31 lattice_0.17-26 >>>>>>> [3] ALL_1.4.7 genefilter_1.28.0 >>>>>>> [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 >>>>>>> [7] KEGG.db_2.3.5 >>>>>>> hugene10sttranscriptcluster.db_4.0.1 >>>>>>> [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >>>>>>> [11] DBI_0.2-4 oligo_1.10.0 >>>>>>> [13] preprocessCore_1.8.0 oligoClasses_1.8.0 >>>>>>> [15] GSEABase_1.8.0 graph_1.24.0 >>>>>>> [17] annotate_1.24.0 AnnotationDbi_1.8.0 >>>>>>> [19] Biobase_2.6.0 loaded via a namespace (and >>>>>>> not attached): >>>>>>> [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 >>>>>>> grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 >>>>>>> splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 XML_2.6-0 >>>>>>> xtable_1.5-5 > >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>>> >>>>>>> >>>>> >>>>> >>> >>> >>> >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 >
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Dear Javier, It might be of interest to you that package xps could handle your problem of removing different control genes, since function rma() has a parameter "exonlevel" for HuGene and HuExon arrays, which allows you to define which probesets to use for rma, e.g. exonlevel="affx+core" will use only probesets of category 'unique', 'similar' and 'mixed' plus the standard AFFX controls, while exonlevel="metacore" will only use probesets of category 'unique', see the help "?exonLevel". Thus there is no need to remove these probesets afterwards. Furthermore, xps has also different methods for non-specific filtering, see help "?PreFilter" Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ Javier P?rez Florido wrote: > Martin Morgan escribi?: >> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: >> >> >>> Hi Javier, >>> >>> Javier P?rez Florido wrote: >>> >>>> Dear list, >>>> I've tried to use the nsFilter function from genefilter package to >>>> perform nonspecific filtering on a Human Gene ST 1.0 dataset. >>>> The expression set has the hugene10sttranscriptcluster.db annotation >>>> package, but when nsFilter is applied: >>>> nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those without >>>> EntrezGene IDs, etc >>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) : >>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found >>>> >>> annotation(subEset) <- "hugene10sttranscriptcluster" >>> >> >> genefilter 1.28.1 should work for both >> "hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster". >> > I've checked that it only works when > > annotation(subEset) <- "hugene10sttranscriptcluster" > > Javier > > >> Martin >> >> >>> Should do the trick. >>> >>> Best, >>> >>> Jim >>> >>> >>> >>>> Maybe nsFilter is not built for this kind of microarrays, although >>>> varFilter,from the same package, works, because it makes use of the >>>> expression values only. >>>> I've made some search on Google, but no success. I can write a >>>> function that removes the different control genes in Human Gene >>>> (AFFX, spike, neg_control,pos_control,etc) and those without >>>> EntrezGene ID, but wanted to know if there is a function that handle >>>> this for this kind of microarrays. >>>> Thanks, >>>> Javier >>>> sessionInfo() >>>> R version 2.10.0 (2009-10-26) >>>> i386-pc-mingw32 >>>> locale: >>>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] >>>> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] >>>> LC_TIME=Spanish_Spain.1252 attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> other attached packages: >>>> [1] Matrix_0.999375-31 lattice_0.17-26 >>>> [3] ALL_1.4.7 genefilter_1.28.0 >>>> [5] pd.hugene.1.0.st.v1_3.0.0 Category_2.12.0 >>>> [7] KEGG.db_2.3.5 >>>> hugene10sttranscriptcluster.db_4.0.1 >>>> [9] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >>>> [11] DBI_0.2-4 oligo_1.10.0 >>>> [13] preprocessCore_1.8.0 oligoClasses_1.8.0 >>>> [15] GSEABase_1.8.0 graph_1.24.0 >>>> [17] annotate_1.24.0 AnnotationDbi_1.8.0 >>>> [19] Biobase_2.6.0 loaded via a namespace (and >>>> not attached): >>>> [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.0 >>>> grid_2.10.0 [5] IRanges_1.4.0 RBGL_1.20.0 >>>> splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 XML_2.6-0 >>>> xtable_1.5-5 > >>>> _______________________________________________ >>>> 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 >>>> >> >> > > _______________________________________________ > 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 >
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