How remove controls probes - Affymetrix Gene
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Hello, I work on affymetrix mouse gene 1.0 ST. I want to know how remove controls probes on Affymetrix Gene. In my studie, I downloaded two files on Affymetrix website: - The Probeset Annotations, CSV Format, Release 32 file (NetAffx Analysis Center -> Exon/Gene -> NetAffy Query -> "Mouse Gene 1.0 ST") - The Transcript Cluster Annotations, CSV, Release 32 file (NetAffx Analysis Center -> Exon/Gene -> NetAffy Query -> "Mouse Gene 1.0 ST") With the first, I had 28 856 main probesets and with second 28 350 main probesets. I add that I run a RMA option "core" with the oligo package. I just want a probe for a probeset. Which file I have to use? (I did'nt use the command getNetAffy because I realized that I lost more probesets! (There were only 28 270 main probes)). Thank you for advance for your answer and your help. Sophie LAMARRE -- output of sessionInfo(): R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 [4] LC_NUMERIC=C LC_TIME=French_France.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] pd.mogene.1.0.st.v1_3.2.0 oligo_1.16.2 preprocessCore_1.14.0 [4] GOstats_2.18.0 RSQLite_0.9-4 DBI_0.2-5 [7] graph_1.30.0 Category_2.18.0 genefilter_1.34.0 [10] gplots_2.8.0 caTools_1.12 bitops_1.0-4.1 [13] gdata_2.8.2 gtools_2.6.2 geneplotter_1.30.0 [16] lattice_0.19-23 annotate_1.30.0 AnnotationDbi_1.14.1 [19] RColorBrewer_1.0-5 ArrayTools_1.12.0 affy_1.30.0 [22] limma_3.8.3 oligoClasses_1.14.0 Biobase_2.12.2 loaded via a namespace (and not attached): [1] affxparser_1.24.0 affyio_1.20.0 Biostrings_2.20.3 bit_1.1-7 ff_2.2-3 [6] GO.db_2.5.0 GSEABase_1.14.0 IRanges_1.10.6 RBGL_1.28.0 splines_2.13.0 [11] survival_2.36-5 tools_2.13.0 XML_3.4-2.2 xtable_1.5-6 -- Sent via the guest posting facility at bioconductor.org.
GO probe oligo GO probe oligo • 758 views
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@james-w-macdonald-5106
Last seen 15 hours ago
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Hi Sophie, On 1/12/2012 11:01 AM, Sophie Lamarre [guest] wrote: > Hello, > > I work on affymetrix mouse gene 1.0 ST. > > I want to know how remove controls probes on Affymetrix Gene. > In my studie, I downloaded two files on Affymetrix website: > - The Probeset Annotations, CSV Format, Release 32 > file (NetAffx Analysis Center -> Exon/Gene -> NetAffy Query -> "Mouse Gene 1.0 ST") > - The Transcript Cluster Annotations, CSV, Release 32 file (NetAffx Analysis Center -> Exon/Gene -> NetAffy Query -> "Mouse Gene 1.0 ST") > > With the first, I had 28 856 main probesets and with second 28 350 main probesets. > > I add that I run a RMA option "core" with the oligo package. I just want a probe for a probeset. I'm not sure what you are asking here. You can't have a probe for a probeset, as there are multiple probes in each probeset. The default for rma() in oligo is to summarize the probesets at the transcript level, which is in general what most people want. You can summarize at the 'probeset' level, which is something like summarizing at the exon level, but if I am not mistaken, there can be more than one probeset per exon, so that gets complicated. Summarizing at the transcript level is an easier path to take. > > Which file I have to use? (I did'nt use the command getNetAffy because I realized that I lost more probesets! (There were only 28 270 main probes)). Rather than getting annotation data from netaffx and then struggling with the format, it is easier to install the mogene10sttranscriptcluster.db package, and use that for annotating your data. There are vignettes in the AnnotationDbi package that show how to use that package. Best, Jim > > Thank you for advance for your answer and your help. > > Sophie LAMARRE > > -- output of sessionInfo(): > > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 > [4] LC_NUMERIC=C LC_TIME=French_France.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.mogene.1.0.st.v1_3.2.0 oligo_1.16.2 preprocessCore_1.14.0 > [4] GOstats_2.18.0 RSQLite_0.9-4 DBI_0.2-5 > [7] graph_1.30.0 Category_2.18.0 genefilter_1.34.0 > [10] gplots_2.8.0 caTools_1.12 bitops_1.0-4.1 > [13] gdata_2.8.2 gtools_2.6.2 geneplotter_1.30.0 > [16] lattice_0.19-23 annotate_1.30.0 AnnotationDbi_1.14.1 > [19] RColorBrewer_1.0-5 ArrayTools_1.12.0 affy_1.30.0 > [22] limma_3.8.3 oligoClasses_1.14.0 Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.24.0 affyio_1.20.0 Biostrings_2.20.3 bit_1.1-7 ff_2.2-3 > [6] GO.db_2.5.0 GSEABase_1.14.0 IRanges_1.10.6 RBGL_1.28.0 splines_2.13.0 > [11] survival_2.36-5 tools_2.13.0 XML_3.4-2.2 xtable_1.5-6 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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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