[BioC] Illumina human ht12 v3 beadchip and illuminaHumanv3BeadID.db

[Manca Marco (PATH)]

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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