[BioC] Illumina human ht12 v3 beadchip and illuminaHumanv3BeadID.db
J.Oosting at lumc.nl
J.Oosting at lumc.nl
Wed Nov 24 16:47:13 CET 2010
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
>
>
>
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