Illumina human ht12 v3 beadchip and illuminaHumanv3BeadID.db
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@manca-marco-path-4295
Last seen 10.2 years ago
Dearest BioConductors, good afternoon. I request your assistance on an issue about which I have found a few old posts but I can't manage to find the solution. I am analyzing an experiment performed by use of Illumina's "human ht12 v3 beadchip" and I am trying now perform some GO and Pathway analysis to make sense of the results I have obtained. The package "of choice" for annotating this chip should be illuminaHumanv3BeadID.db (but I have similar results with lumiHumanAll.db after converting Illumina probes' IDs to NuIDs): the chip has apparently 48803 probes, while I can obtain annotations for roughly 27500 of them > qcdata = capture.output(illuminaHumanv3BeadID()) > head(qcdata, 35) [1] "Quality control information for illuminaHumanv3BeadID:" [2] "" [3] "" [4] "This package has the following mappings:" [5] "" [6] "illuminaHumanv3BeadIDACCNUM has 27570 mapped keys (of 27570 keys)" [7] "illuminaHumanv3BeadIDALIAS2PROBE has 67274 mapped keys (of 109070 keys)" [8] "illuminaHumanv3BeadIDCHR has 25726 mapped keys (of 27570 keys)" [9] "illuminaHumanv3BeadIDCHRLENGTHS has 25 mapped keys (of 25 keys)" [10] "illuminaHumanv3BeadIDCHRLOC has 24916 mapped keys (of 27570 keys)" [11] "illuminaHumanv3BeadIDCHRLOCEND has 24916 mapped keys (of 27570 keys)" [12] "illuminaHumanv3BeadIDENSEMBL has 24681 mapped keys (of 27570 keys)" [13] "illuminaHumanv3BeadIDENSEMBL2PROBE has 17009 mapped keys (of 19892 keys)" [14] "illuminaHumanv3BeadIDENTREZID has 25726 mapped keys (of 27570 keys)" [15] "illuminaHumanv3BeadIDENZYME has 2890 mapped keys (of 27570 keys)" [16] "illuminaHumanv3BeadIDENZYME2PROBE has 857 mapped keys (of 901 keys)" [17] "illuminaHumanv3BeadIDGENENAME has 25726 mapped keys (of 27570 keys)" [18] "illuminaHumanv3BeadIDGO has 22807 mapped keys (of 27570 keys)" [19] "illuminaHumanv3BeadIDGO2ALLPROBES has 11021 mapped keys (of 11236 keys)" [20] "illuminaHumanv3BeadIDGO2PROBE has 8010 mapped keys (of 8245 keys)" [21] "illuminaHumanv3BeadIDMAP has 25589 mapped keys (of 27570 keys)" [22] "illuminaHumanv3BeadIDOMIM has 17688 mapped keys (of 27570 keys)" [23] "illuminaHumanv3BeadIDPATH has 7029 mapped keys (of 27570 keys)" [24] "illuminaHumanv3BeadIDPATH2PROBE has 220 mapped keys (of 220 keys)" [25] "illuminaHumanv3BeadIDPFAM has 25262 mapped keys (of 27570 keys)" [26] "illuminaHumanv3BeadIDPMID has 25101 mapped keys (of 27570 keys)" [27] "illuminaHumanv3BeadIDPMID2PROBE has 231447 mapped keys (of 248847 keys)" [28] "illuminaHumanv3BeadIDPROSITE has 25262 mapped keys (of 27570 keys)" [29] "illuminaHumanv3BeadIDREFSEQ has 25726 mapped keys (of 27570 keys)" [30] "illuminaHumanv3BeadIDSYMBOL has 25726 mapped keys (of 27570 keys)" [31] "illuminaHumanv3BeadIDUNIGENE has 25256 mapped keys (of 27570 keys)" [32] "illuminaHumanv3BeadIDUNIPROT has 24730 mapped keys (of 27570 keys)" [33] "" [34] "" [35] "Additional Information about this package:" My sessionInfo() is as follows: > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] SPIA_1.4.0 RCurl_1.4-3 [3] bitops_1.0-4.1 annaffy_1.18.0 [5] KEGG.db_2.3.5 GO.db_2.3.5 [7] limma_3.2.3 illuminaHumanv3BeadID.db_1.4.1 [9] org.Hs.eg.db_2.3.6 lumi_1.12.4 [11] MASS_7.3-7 RSQLite_0.9-2 [13] DBI_0.2-5 preprocessCore_1.8.0 [15] mgcv_1.6-2 affy_1.24.2 [17] annotate_1.24.1 AnnotationDbi_1.8.2 [19] Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 grid_2.10.1 lattice_0.18-3 Matrix_0.999375-44 [5] nlme_3.1-97 tools_2.10.1 xtable_1.5-6 > Thank you in advance for any hints to how to solve the problem (or to why I see this discrepancy) Best regards, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confide...{{dropped:15}}
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@oosting-j-path-412
Last seen 10.2 years ago
This is normal for this chiptype. The HT12 contains a lot of probes that have no proper annotation. These are mostly ESTs that have been submitted to Genbank at some time, but have never been properly attributed to any gene. For most types of analysis these extra probes are basically worthless, so I usually exclude them before the statistical analysis. Jan > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- > bounces at stat.math.ethz.ch] On Behalf Of Manca Marco (PATH) > Sent: woensdag 24 november 2010 16:01 > To: bioconductor mailing list > Subject: [BioC] Illumina human ht12 v3 beadchip and > illuminaHumanv3BeadID.db > Importance: High > > > > Dearest BioConductors, > > good afternoon. > > I request your assistance on an issue about which I have found a few old > posts but I can't manage to find the solution. > > I am analyzing an experiment performed by use of Illumina's "human ht12 v3 > beadchip" and I am trying now perform some GO and Pathway analysis to make > sense of the results I have obtained. > > The package "of choice" for annotating this chip should be > illuminaHumanv3BeadID.db (but I have similar results with lumiHumanAll.db > after converting Illumina probes' IDs to NuIDs): the chip has apparently > 48803 probes, while I can obtain annotations for roughly 27500 of them > > > qcdata = capture.output(illuminaHumanv3BeadID()) > > head(qcdata, 35) > [1] "Quality control information for illuminaHumanv3BeadID:" > [2] "" > [3] "" > [4] "This package has the following mappings:" > [5] "" > [6] "illuminaHumanv3BeadIDACCNUM has 27570 mapped keys (of 27570 keys)" > [7] "illuminaHumanv3BeadIDALIAS2PROBE has 67274 mapped keys (of 109070 > keys)" > [8] "illuminaHumanv3BeadIDCHR has 25726 mapped keys (of 27570 keys)" > [9] "illuminaHumanv3BeadIDCHRLENGTHS has 25 mapped keys (of 25 keys)" > [10] "illuminaHumanv3BeadIDCHRLOC has 24916 mapped keys (of 27570 keys)" > [11] "illuminaHumanv3BeadIDCHRLOCEND has 24916 mapped keys (of 27570 > keys)" > [12] "illuminaHumanv3BeadIDENSEMBL has 24681 mapped keys (of 27570 keys)" > [13] "illuminaHumanv3BeadIDENSEMBL2PROBE has 17009 mapped keys (of 19892 > keys)" > [14] "illuminaHumanv3BeadIDENTREZID has 25726 mapped keys (of 27570 keys)" > [15] "illuminaHumanv3BeadIDENZYME has 2890 mapped keys (of 27570 keys)" > [16] "illuminaHumanv3BeadIDENZYME2PROBE has 857 mapped keys (of 901 keys)" > [17] "illuminaHumanv3BeadIDGENENAME has 25726 mapped keys (of 27570 keys)" > [18] "illuminaHumanv3BeadIDGO has 22807 mapped keys (of 27570 keys)" > [19] "illuminaHumanv3BeadIDGO2ALLPROBES has 11021 mapped keys (of 11236 > keys)" > [20] "illuminaHumanv3BeadIDGO2PROBE has 8010 mapped keys (of 8245 keys)" > [21] "illuminaHumanv3BeadIDMAP has 25589 mapped keys (of 27570 keys)" > [22] "illuminaHumanv3BeadIDOMIM has 17688 mapped keys (of 27570 keys)" > [23] "illuminaHumanv3BeadIDPATH has 7029 mapped keys (of 27570 keys)" > [24] "illuminaHumanv3BeadIDPATH2PROBE has 220 mapped keys (of 220 keys)" > [25] "illuminaHumanv3BeadIDPFAM has 25262 mapped keys (of 27570 keys)" > [26] "illuminaHumanv3BeadIDPMID has 25101 mapped keys (of 27570 keys)" > [27] "illuminaHumanv3BeadIDPMID2PROBE has 231447 mapped keys (of 248847 > keys)" > [28] "illuminaHumanv3BeadIDPROSITE has 25262 mapped keys (of 27570 keys)" > [29] "illuminaHumanv3BeadIDREFSEQ has 25726 mapped keys (of 27570 keys)" > [30] "illuminaHumanv3BeadIDSYMBOL has 25726 mapped keys (of 27570 keys)" > [31] "illuminaHumanv3BeadIDUNIGENE has 25256 mapped keys (of 27570 keys)" > [32] "illuminaHumanv3BeadIDUNIPROT has 24730 mapped keys (of 27570 keys)" > [33] "" > [34] "" > [35] "Additional Information about this package:" > > My sessionInfo() is as follows: > > > sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] SPIA_1.4.0 RCurl_1.4-3 > [3] bitops_1.0-4.1 annaffy_1.18.0 > [5] KEGG.db_2.3.5 GO.db_2.3.5 > [7] limma_3.2.3 illuminaHumanv3BeadID.db_1.4.1 > [9] org.Hs.eg.db_2.3.6 lumi_1.12.4 > [11] MASS_7.3-7 RSQLite_0.9-2 > [13] DBI_0.2-5 preprocessCore_1.8.0 > [15] mgcv_1.6-2 affy_1.24.2 > [17] annotate_1.24.1 AnnotationDbi_1.8.2 > [19] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 grid_2.10.1 lattice_0.18-3 > Matrix_0.999375-44 > [5] nlme_3.1-97 tools_2.10.1 xtable_1.5-6 > > > > > > > Thank you in advance for any hints to how to solve the problem (or to why > I see this discrepancy) > > Best regards, Marco > > > -- > Marco Manca, MD > University of Maastricht > Faculty of Health, Medicine and Life Sciences (FHML) > Cardiovascular Research Institute (CARIM) > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology > - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 > HX Maastricht > > E-mail: m.manca at maastrichtuniversity.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > ********************************************************************** ** ** > ******************************************* > > This email and any files transmitted with it are confide...{{dropped:15}} > > _______________________________________________ > 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 Jan, thank you for your prompt reply. Can I blatantly ask why are these probes included in the chip if so? Yet I have been comparing the results I obtain in BioConductor with those of a colleague who is analyzing data obtained with the same chip but using Ingenuity Pathway Analysis and she is apparently missing only a few hundreds annotation rather than my tens of thousands... Is Ingenuity doing something wrong here (like attributing annotations based on imperfect alignments?) or shall I abide to those results and leave R/BioConductor for these datasets? Thank you in advance for any insight you will share with me. Best regards, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: J.Oosting at lumc.nl [J.Oosting at lumc.nl] Inviato: mercoled? 24 novembre 2010 16.47 A: Manca Marco (PATH); bioconductor at stat.math.ethz.ch Oggetto: RE: [BioC] Illumina human ht12 v3 beadchip and illuminaHumanv3BeadID.db This is normal for this chiptype. The HT12 contains a lot of probes that have no proper annotation. These are mostly ESTs that have been submitted to Genbank at some time, but have never been properly attributed to any gene. For most types of analysis these extra probes are basically worthless, so I usually exclude them before the statistical analysis. Jan > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- > bounces at stat.math.ethz.ch] On Behalf Of Manca Marco (PATH) > Sent: woensdag 24 november 2010 16:01 > To: bioconductor mailing list > Subject: [BioC] Illumina human ht12 v3 beadchip and > illuminaHumanv3BeadID.db > Importance: High > > > > Dearest BioConductors, > > good afternoon. > > I request your assistance on an issue about which I have found a few old > posts but I can't manage to find the solution. > > I am analyzing an experiment performed by use of Illumina's "human ht12 v3 > beadchip" and I am trying now perform some GO and Pathway analysis to make > sense of the results I have obtained. > > The package "of choice" for annotating this chip should be > illuminaHumanv3BeadID.db (but I have similar results with lumiHumanAll.db > after converting Illumina probes' IDs to NuIDs): the chip has apparently > 48803 probes, while I can obtain annotations for roughly 27500 of them > > > qcdata = capture.output(illuminaHumanv3BeadID()) > > head(qcdata, 35) > [1] "Quality control information for illuminaHumanv3BeadID:" > [2] "" > [3] "" > [4] "This package has the following mappings:" > [5] "" > [6] "illuminaHumanv3BeadIDACCNUM has 27570 mapped keys (of 27570 keys)" > [7] "illuminaHumanv3BeadIDALIAS2PROBE has 67274 mapped keys (of 109070 > keys)" > [8] "illuminaHumanv3BeadIDCHR has 25726 mapped keys (of 27570 keys)" > [9] "illuminaHumanv3BeadIDCHRLENGTHS has 25 mapped keys (of 25 keys)" > [10] "illuminaHumanv3BeadIDCHRLOC has 24916 mapped keys (of 27570 keys)" > [11] "illuminaHumanv3BeadIDCHRLOCEND has 24916 mapped keys (of 27570 > keys)" > [12] "illuminaHumanv3BeadIDENSEMBL has 24681 mapped keys (of 27570 keys)" > [13] "illuminaHumanv3BeadIDENSEMBL2PROBE has 17009 mapped keys (of 19892 > keys)" > [14] "illuminaHumanv3BeadIDENTREZID has 25726 mapped keys (of 27570 keys)" > [15] "illuminaHumanv3BeadIDENZYME has 2890 mapped keys (of 27570 keys)" > [16] "illuminaHumanv3BeadIDENZYME2PROBE has 857 mapped keys (of 901 keys)" > [17] "illuminaHumanv3BeadIDGENENAME has 25726 mapped keys (of 27570 keys)" > [18] "illuminaHumanv3BeadIDGO has 22807 mapped keys (of 27570 keys)" > [19] "illuminaHumanv3BeadIDGO2ALLPROBES has 11021 mapped keys (of 11236 > keys)" > [20] "illuminaHumanv3BeadIDGO2PROBE has 8010 mapped keys (of 8245 keys)" > [21] "illuminaHumanv3BeadIDMAP has 25589 mapped keys (of 27570 keys)" > [22] "illuminaHumanv3BeadIDOMIM has 17688 mapped keys (of 27570 keys)" > [23] "illuminaHumanv3BeadIDPATH has 7029 mapped keys (of 27570 keys)" > [24] "illuminaHumanv3BeadIDPATH2PROBE has 220 mapped keys (of 220 keys)" > [25] "illuminaHumanv3BeadIDPFAM has 25262 mapped keys (of 27570 keys)" > [26] "illuminaHumanv3BeadIDPMID has 25101 mapped keys (of 27570 keys)" > [27] "illuminaHumanv3BeadIDPMID2PROBE has 231447 mapped keys (of 248847 > keys)" > [28] "illuminaHumanv3BeadIDPROSITE has 25262 mapped keys (of 27570 keys)" > [29] "illuminaHumanv3BeadIDREFSEQ has 25726 mapped keys (of 27570 keys)" > [30] "illuminaHumanv3BeadIDSYMBOL has 25726 mapped keys (of 27570 keys)" > [31] "illuminaHumanv3BeadIDUNIGENE has 25256 mapped keys (of 27570 keys)" > [32] "illuminaHumanv3BeadIDUNIPROT has 24730 mapped keys (of 27570 keys)" > [33] "" > [34] "" > [35] "Additional Information about this package:" > > My sessionInfo() is as follows: > > > sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] SPIA_1.4.0 RCurl_1.4-3 > [3] bitops_1.0-4.1 annaffy_1.18.0 > [5] KEGG.db_2.3.5 GO.db_2.3.5 > [7] limma_3.2.3 illuminaHumanv3BeadID.db_1.4.1 > [9] org.Hs.eg.db_2.3.6 lumi_1.12.4 > [11] MASS_7.3-7 RSQLite_0.9-2 > [13] DBI_0.2-5 preprocessCore_1.8.0 > [15] mgcv_1.6-2 affy_1.24.2 > [17] annotate_1.24.1 AnnotationDbi_1.8.2 > [19] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 grid_2.10.1 lattice_0.18-3 > Matrix_0.999375-44 > [5] nlme_3.1-97 tools_2.10.1 xtable_1.5-6 > > > > > > > Thank you in advance for any hints to how to solve the problem (or to why > I see this discrepancy) > > Best regards, Marco > > > -- > Marco Manca, MD > University of Maastricht > Faculty of Health, Medicine and Life Sciences (FHML) > Cardiovascular Research Institute (CARIM) > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology > - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 > HX Maastricht > > E-mail: m.manca at maastrichtuniversity.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > ********************************************************************** ** ** > ******************************************* > > This email and any files transmitted with it are confide...{{dropped:15}} > > _______________________________________________ > 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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Can I even more blatantly ask a related question? Please excuse my inexperience. Using Affymetrix Canine 2 chips comparing brain tumor and brain normal control samples in dogs, I've been doing gene set enrichment analyses using Ingenuity IPA and Bioconductor GOstats with all three GO ontologies and KEGG. From a brief look and my first attempt at this comparison, the results seem very different and mostly Ingenuity is providing disease/cancer categories which I cannot get through GO and KEGG? Many thanks for any comments. Ina ----- Original Message ----- From: "Manca Marco (PATH)" <m.manca@maastrichtuniversity.nl> To: "J Oosting" <j.oosting at="" lumc.nl="">, bioconductor at stat.math.ethz.ch Sent: Wednesday, November 24, 2010 11:05:12 AM Subject: [BioC] R: Illumina human ht12 v3 beadchip and illuminaHumanv3BeadID.db Dear Jan, thank you for your prompt reply. Can I blatantly ask why are these probes included in the chip if so? Yet I have been comparing the results I obtain in BioConductor with those of a colleague who is analyzing data obtained with the same chip but using Ingenuity Pathway Analysis and she is apparently missing only a few hundreds annotation rather than my tens of thousands... Is Ingenuity doing something wrong here (like attributing annotations based on imperfect alignments?) or shall I abide to those results and leave R/BioConductor for these datasets? Thank you in advance for any insight you will share with me. Best regards, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: J.Oosting at lumc.nl [J.Oosting at lumc.nl] Inviato: mercoled? 24 novembre 2010 16.47 A: Manca Marco (PATH); bioconductor at stat.math.ethz.ch Oggetto: RE: [BioC] Illumina human ht12 v3 beadchip and illuminaHumanv3BeadID.db This is normal for this chiptype. The HT12 contains a lot of probes that have no proper annotation. These are mostly ESTs that have been submitted to Genbank at some time, but have never been properly attributed to any gene. For most types of analysis these extra probes are basically worthless, so I usually exclude them before the statistical analysis. Jan > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- > bounces at stat.math.ethz.ch] On Behalf Of Manca Marco (PATH) > Sent: woensdag 24 november 2010 16:01 > To: bioconductor mailing list > Subject: [BioC] Illumina human ht12 v3 beadchip and > illuminaHumanv3BeadID.db > Importance: High > > > > Dearest BioConductors, > > good afternoon. > > I request your assistance on an issue about which I have found a few old > posts but I can't manage to find the solution. > > I am analyzing an experiment performed by use of Illumina's "human ht12 v3 > beadchip" and I am trying now perform some GO and Pathway analysis to make > sense of the results I have obtained. > > The package "of choice" for annotating this chip should be > illuminaHumanv3BeadID.db (but I have similar results with lumiHumanAll.db > after converting Illumina probes' IDs to NuIDs): the chip has apparently > 48803 probes, while I can obtain annotations for roughly 27500 of them > > > qcdata = capture.output(illuminaHumanv3BeadID()) > > head(qcdata, 35) > [1] "Quality control information for illuminaHumanv3BeadID:" > [2] "" > [3] "" > [4] "This package has the following mappings:" > [5] "" > [6] "illuminaHumanv3BeadIDACCNUM has 27570 mapped keys (of 27570 keys)" > [7] "illuminaHumanv3BeadIDALIAS2PROBE has 67274 mapped keys (of 109070 > keys)" > [8] "illuminaHumanv3BeadIDCHR has 25726 mapped keys (of 27570 keys)" > [9] "illuminaHumanv3BeadIDCHRLENGTHS has 25 mapped keys (of 25 keys)" > [10] "illuminaHumanv3BeadIDCHRLOC has 24916 mapped keys (of 27570 keys)" > [11] "illuminaHumanv3BeadIDCHRLOCEND has 24916 mapped keys (of 27570 > keys)" > [12] "illuminaHumanv3BeadIDENSEMBL has 24681 mapped keys (of 27570 keys)" > [13] "illuminaHumanv3BeadIDENSEMBL2PROBE has 17009 mapped keys (of 19892 > keys)" > [14] "illuminaHumanv3BeadIDENTREZID has 25726 mapped keys (of 27570 keys)" > [15] "illuminaHumanv3BeadIDENZYME has 2890 mapped keys (of 27570 keys)" > [16] "illuminaHumanv3BeadIDENZYME2PROBE has 857 mapped keys (of 901 keys)" > [17] "illuminaHumanv3BeadIDGENENAME has 25726 mapped keys (of 27570 keys)" > [18] "illuminaHumanv3BeadIDGO has 22807 mapped keys (of 27570 keys)" > [19] "illuminaHumanv3BeadIDGO2ALLPROBES has 11021 mapped keys (of 11236 > keys)" > [20] "illuminaHumanv3BeadIDGO2PROBE has 8010 mapped keys (of 8245 keys)" > [21] "illuminaHumanv3BeadIDMAP has 25589 mapped keys (of 27570 keys)" > [22] "illuminaHumanv3BeadIDOMIM has 17688 mapped keys (of 27570 keys)" > [23] "illuminaHumanv3BeadIDPATH has 7029 mapped keys (of 27570 keys)" > [24] "illuminaHumanv3BeadIDPATH2PROBE has 220 mapped keys (of 220 keys)" > [25] "illuminaHumanv3BeadIDPFAM has 25262 mapped keys (of 27570 keys)" > [26] "illuminaHumanv3BeadIDPMID has 25101 mapped keys (of 27570 keys)" > [27] "illuminaHumanv3BeadIDPMID2PROBE has 231447 mapped keys (of 248847 > keys)" > [28] "illuminaHumanv3BeadIDPROSITE has 25262 mapped keys (of 27570 keys)" > [29] "illuminaHumanv3BeadIDREFSEQ has 25726 mapped keys (of 27570 keys)" > [30] "illuminaHumanv3BeadIDSYMBOL has 25726 mapped keys (of 27570 keys)" > [31] "illuminaHumanv3BeadIDUNIGENE has 25256 mapped keys (of 27570 keys)" > [32] "illuminaHumanv3BeadIDUNIPROT has 24730 mapped keys (of 27570 keys)" > [33] "" > [34] "" > [35] "Additional Information about this package:" > > My sessionInfo() is as follows: > > > sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] SPIA_1.4.0 RCurl_1.4-3 > [3] bitops_1.0-4.1 annaffy_1.18.0 > [5] KEGG.db_2.3.5 GO.db_2.3.5 > [7] limma_3.2.3 illuminaHumanv3BeadID.db_1.4.1 > [9] org.Hs.eg.db_2.3.6 lumi_1.12.4 > [11] MASS_7.3-7 RSQLite_0.9-2 > [13] DBI_0.2-5 preprocessCore_1.8.0 > [15] mgcv_1.6-2 affy_1.24.2 > [17] annotate_1.24.1 AnnotationDbi_1.8.2 > [19] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 grid_2.10.1 lattice_0.18-3 > Matrix_0.999375-44 > [5] nlme_3.1-97 tools_2.10.1 xtable_1.5-6 > > > > > > > Thank you in advance for any hints to how to solve the problem (or to why > I see this discrepancy) > > Best regards, Marco > > > -- > Marco Manca, MD > University of Maastricht > Faculty of Health, Medicine and Life Sciences (FHML) > Cardiovascular Research Institute (CARIM) > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology > - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 > HX Maastricht > > E-mail: m.manca at maastrichtuniversity.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > ********************************************************************** ** ** > ******************************************* > > This email and any files transmitted with it are confide...{{dropped:15}} > > _______________________________________________ > 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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On Wed, Nov 24, 2010 at 11:16 AM, Ina Hoeschele <inah@vbi.vt.edu> wrote: > Can I even more blatantly ask a related question? Please excuse my > inexperience. Using Affymetrix Canine 2 chips comparing brain tumor and > brain normal control samples in dogs, I've been doing gene set enrichment > analyses using Ingenuity IPA and Bioconductor GOstats with all three GO > ontologies and KEGG. From a brief look and my first attempt at this > comparison, the results seem very different and mostly Ingenuity is > providing disease/cancer categories which I cannot get through GO and KEGG? > Hi, Ina. GO and KEGG do not provide disease and cancer categories per se, so it will not be possible to compare the results directly. More generally, IPA and GOstats (or other gene set tools) will give different views of the biological relevance of your data. In my experience, neither is perfect, so using both to generate hypotheses can be useful. Sean > Many thanks for any comments. > Ina > > ----- Original Message ----- > From: "Manca Marco (PATH)" <m.manca@maastrichtuniversity.nl> > To: "J Oosting" <j.oosting@lumc.nl>, bioconductor@stat.math.ethz.ch > Sent: Wednesday, November 24, 2010 11:05:12 AM > Subject: [BioC] R: Illumina human ht12 v3 beadchip and > illuminaHumanv3BeadID.db > > > > Dear Jan, > > thank you for your prompt reply. > > Can I blatantly ask why are these probes included in the chip if so? > > Yet I have been comparing the results I obtain in BioConductor with those > of a colleague who is analyzing data obtained with the same chip but using > Ingenuity Pathway Analysis and she is apparently missing only a few hundreds > annotation rather than my tens of thousands... Is Ingenuity doing something > wrong here (like attributing annotations based on imperfect alignments?) or > shall I abide to those results and leave R/BioConductor for these datasets? > > Thank you in advance for any insight you will share with me. > > Best regards, Marco > > -- > Marco Manca, MD > University of Maastricht > Faculty of Health, Medicine and Life Sciences (FHML) > Cardiovascular Research Institute (CARIM) > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology > - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX > Maastricht > > E-mail: m.manca@maastrichtuniversity.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > > ******************************************************************** ************************************************* > > This email and any files transmitted with it are confidential and solely > for the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. > If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received > this email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on > +31626441205 Dr Marco MANCA > > > ******************************************************************** ************************************************* > ________________________________________ > Da: J.Oosting@lumc.nl [J.Oosting@lumc.nl] > Inviato: mercoledì 24 novembre 2010 16.47 > A: Manca Marco (PATH); bioconductor@stat.math.ethz.ch > Oggetto: RE: [BioC] Illumina human ht12 v3 beadchip and > illuminaHumanv3BeadID.db > > This is normal for this chiptype. The HT12 contains a lot of probes that > have no proper annotation. These are mostly ESTs that have been > submitted to Genbank at some time, but have never been properly > attributed to any gene. > > For most types of analysis these extra probes are basically worthless, > so I usually exclude them before the statistical analysis. > > Jan > > > > -----Original Message----- > > From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- > > bounces@stat.math.ethz.ch] On Behalf Of Manca Marco (PATH) > > Sent: woensdag 24 november 2010 16:01 > > To: bioconductor mailing list > > Subject: [BioC] Illumina human ht12 v3 beadchip and > > illuminaHumanv3BeadID.db > > Importance: High > > > > > > > > Dearest BioConductors, > > > > good afternoon. > > > > I request your assistance on an issue about which I have found a few > old > > posts but I can't manage to find the solution. > > > > I am analyzing an experiment performed by use of Illumina's "human > ht12 v3 > > beadchip" and I am trying now perform some GO and Pathway analysis to > make > > sense of the results I have obtained. > > > > The package "of choice" for annotating this chip should be > > illuminaHumanv3BeadID.db (but I have similar results with > lumiHumanAll.db > > after converting Illumina probes' IDs to NuIDs): the chip has > apparently > > 48803 probes, while I can obtain annotations for roughly 27500 of them > > > > > qcdata = capture.output(illuminaHumanv3BeadID()) > > > head(qcdata, 35) > > [1] "Quality control information for illuminaHumanv3BeadID:" > > [2] "" > > [3] "" > > [4] "This package has the following mappings:" > > [5] "" > > [6] "illuminaHumanv3BeadIDACCNUM has 27570 mapped keys (of 27570 > keys)" > > [7] "illuminaHumanv3BeadIDALIAS2PROBE has 67274 mapped keys (of > 109070 > > keys)" > > [8] "illuminaHumanv3BeadIDCHR has 25726 mapped keys (of 27570 keys)" > > [9] "illuminaHumanv3BeadIDCHRLENGTHS has 25 mapped keys (of 25 keys)" > > [10] "illuminaHumanv3BeadIDCHRLOC has 24916 mapped keys (of 27570 > keys)" > > [11] "illuminaHumanv3BeadIDCHRLOCEND has 24916 mapped keys (of 27570 > > keys)" > > [12] "illuminaHumanv3BeadIDENSEMBL has 24681 mapped keys (of 27570 > keys)" > > [13] "illuminaHumanv3BeadIDENSEMBL2PROBE has 17009 mapped keys (of > 19892 > > keys)" > > [14] "illuminaHumanv3BeadIDENTREZID has 25726 mapped keys (of 27570 > keys)" > > [15] "illuminaHumanv3BeadIDENZYME has 2890 mapped keys (of 27570 > keys)" > > [16] "illuminaHumanv3BeadIDENZYME2PROBE has 857 mapped keys (of 901 > keys)" > > [17] "illuminaHumanv3BeadIDGENENAME has 25726 mapped keys (of 27570 > keys)" > > [18] "illuminaHumanv3BeadIDGO has 22807 mapped keys (of 27570 keys)" > > [19] "illuminaHumanv3BeadIDGO2ALLPROBES has 11021 mapped keys (of > 11236 > > keys)" > > [20] "illuminaHumanv3BeadIDGO2PROBE has 8010 mapped keys (of 8245 > keys)" > > [21] "illuminaHumanv3BeadIDMAP has 25589 mapped keys (of 27570 keys)" > > [22] "illuminaHumanv3BeadIDOMIM has 17688 mapped keys (of 27570 keys)" > > [23] "illuminaHumanv3BeadIDPATH has 7029 mapped keys (of 27570 keys)" > > [24] "illuminaHumanv3BeadIDPATH2PROBE has 220 mapped keys (of 220 > keys)" > > [25] "illuminaHumanv3BeadIDPFAM has 25262 mapped keys (of 27570 keys)" > > [26] "illuminaHumanv3BeadIDPMID has 25101 mapped keys (of 27570 keys)" > > [27] "illuminaHumanv3BeadIDPMID2PROBE has 231447 mapped keys (of > 248847 > > keys)" > > [28] "illuminaHumanv3BeadIDPROSITE has 25262 mapped keys (of 27570 > keys)" > > [29] "illuminaHumanv3BeadIDREFSEQ has 25726 mapped keys (of 27570 > keys)" > > [30] "illuminaHumanv3BeadIDSYMBOL has 25726 mapped keys (of 27570 > keys)" > > [31] "illuminaHumanv3BeadIDUNIGENE has 25256 mapped keys (of 27570 > keys)" > > [32] "illuminaHumanv3BeadIDUNIPROT has 24730 mapped keys (of 27570 > keys)" > > [33] "" > > [34] "" > > [35] "Additional Information about this package:" > > > > My sessionInfo() is as follows: > > > > > sessionInfo() > > R version 2.10.1 (2009-12-14) > > x86_64-pc-linux-gnu > > > > locale: > > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > > [7] LC_PAPER=en_US.utf8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] SPIA_1.4.0 RCurl_1.4-3 > > [3] bitops_1.0-4.1 annaffy_1.18.0 > > [5] KEGG.db_2.3.5 GO.db_2.3.5 > > [7] limma_3.2.3 illuminaHumanv3BeadID.db_1.4.1 > > [9] org.Hs.eg.db_2.3.6 lumi_1.12.4 > > [11] MASS_7.3-7 RSQLite_0.9-2 > > [13] DBI_0.2-5 preprocessCore_1.8.0 > > [15] mgcv_1.6-2 affy_1.24.2 > > [17] annotate_1.24.1 AnnotationDbi_1.8.2 > > [19] Biobase_2.6.1 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.14.0 grid_2.10.1 lattice_0.18-3 > > Matrix_0.999375-44 > > [5] nlme_3.1-97 tools_2.10.1 xtable_1.5-6 > > > > > > > > > > > > > Thank you in advance for any hints to how to solve the problem (or to > why > > I see this discrepancy) > > > > Best regards, Marco > > > > > > -- > > Marco Manca, MD > > University of Maastricht > > Faculty of Health, Medicine and Life Sciences (FHML) > > Cardiovascular Research Institute (CARIM) > > > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > > Visiting address: Experimental Vascular Pathology group, Dept of > Pathology > > - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, > 6229 > > HX Maastricht > > > > E-mail: m.manca@maastrichtuniversity.nl > > Office telephone: +31(0)433874633 > > Personal mobile: +31(0)626441205 > > Twitter: @markomanka > > > > > > > ******************************************************************** **** > ** > > ******************************************* > > > > This email and any files transmitted with it are > confide...{{dropped:15}} > > > > _______________________________________________ > > 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 > > _______________________________________________ > 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 > > _______________________________________________ > 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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