Dear list,
I've read the illuminaHumanv4.db.pdf, and it's not clear to me how the mappings are built. From the short package description, I thought the RefSeq ID's from the illumina array manifest would be used, but according to the pdf manual, I think its ACCNUM, but we're not told from where the ACCNUM is derived (from ?illuminaHumanv4ACCNUM: "For chip packages such as this, the ACCNUM mapping comes directly from the manufacturer.").

I raise the question, since within the illuminaHuman4SYMBOL table, there are no probes for the CTNND1 gene, whereas according to the manifest file, there are 5 probes that should map to that gene:

from the manifest:
$ grep -w CTNND1 HumanHT-12_V4_0_R2_15002873_B.txt | cut -f3,6,5,14
#Search_Key	ILMN_Gene	RefSeq_ID	Symbol
XM_943087.1	CTNND1	XM_943087.1	ILMN_1651944
XM_937008.1	CTNND1	XM_937008.1	ILMN_1807510
XM_943098.1	CTNND1	NM_001085458.1	ILMN_1696806
XM_943098.1	CTNND1	XM_943098.1	ILMN_1663159
NM_001331.1	CTNND1	NM_001331.1	ILMN_2293511

# from the illuminaHumanv4.db package
require(illuminaHumanv4.db)
> ids <- c("ILMN_1651944", "ILMN_1807510", "ILMN_1696806", "ILMN_1663159", "ILMN_2293511")
> unlist(mget(ids, illuminaHumanv4SYMBOL))
ILMN_1651944 ILMN_1807510 ILMN_1696806 ILMN_1663159 ILMN_2293511 
          NA           NA           NA           NA           NA 
> unlist(mget(ids, illuminaHumanv4REFSEQ))
ILMN_1651944 ILMN_1807510 ILMN_1696806 ILMN_1663159 ILMN_2293511 
          NA           NA           NA           NA           NA 
# why are there no REFSEQID's for these probes?

> mget(ids, illuminaHumanv4ACCNUM)
$ILMN_1651944
[1] NA
$ILMN_1807510
[1] NA
$ILMN_1696806
 [1] "NM_001085458" "NM_001085459" "NM_001085460" "NM_001085461" "NM_001085462"
 [6] "NM_001085463" "NM_001085464" "NM_001085465" "NM_001085466" "NM_001085467"
[11] "NM_001085468" "NM_001085469" "NM_001331"    "NR_037646"   
$ILMN_1663159
[1] NA
$ILMN_2293511
 [1] "NM_001085458" "NM_001085459" "NM_001085460" "NM_001085461" "NM_001085462"
 [6] "NM_001085463" "NM_001085464" "NM_001085465" "NM_001085466" "NM_001085467"
[11] "NM_001085468" "NM_001085469" "NM_001331"    "NR_037646"   

# all of these RefSeq ID's correspond to Entrez Gene ID 1500, CTNND1 catenin (cadherin-associated protein), delta 1 [ Homo sapiens ]
# why do 3 probes not have an ACCNUM?


If I BLAST all 5 probes, the 3 probes with NA in the ACCNUM (see above) all align to NG_029078.1 (=CTNND1), but not to NM_001331 (=CTNND1), and the 2 probes with lots of ACCNUM ID's align to both NG_029078.1 and NM_001331 amongst many others.
mget(ids, illuminaHumanv4PROBESEQUENCE)
>ILMN_1651944 -> NG_029078.1
GAAGGACCCTCCCCCGCTTCATAGTTTATGAATGCGAGAGTTGGTAAGGG
>ILMN_1807510 -> NG_029078.1
CGGTCATTCTCTGCCATCCCTAGAAAGAATGTCCAATCCACTGCCTTTGT
>ILMN_1696806 -> NG_029078.1, NM_001331, many others
GACCATCCCAAAAAGGAAGTGCACCTTGGAGCCTGTGGAGCTCTCAAGAA
>ILMN_1663159 -> NG_029078.1
GCCTATTCTTTAGCCTCCATTCCTATCTGTATTGCATACTGTAACTCCAA
>ILMN_2293511 -> NG_029078.1, NM_001331, many others
ATCCAGACTTTGGGTCGTGATTTCCGCAAGAATGGCAATGGGGGACCTGG



I'd really love to get to the bottom of this, as the R annotation packages are very rich, but missing ID's make it hard to know whether they're better than the manufacturers manifest files.

cheers,
Mark
-----------------------------------------------------
Mark Cowley, PhD

Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-----------------------------------------------------


> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] graphics  datasets  grDevices utils     grid      stats     methods 
[8] base     

other attached packages:
 [1] illuminaHumanv4.db_1.10.0 org.Hs.eg.db_2.5.0       
 [3] RSQLite_0.9-4             DBI_0.2-5                
 [5] AnnotationDbi_1.14.1      limma_3.8.3              
 [7] mjcdev_1.0                Cairo_1.4-9              
 [9] metaGSEA_1.0.2            pwbc_1.0.3               
[11] lumidat_1.0.1             lumi_2.4.0               
[13] nleqslv_1.8.6             updateR_1.0.4            
[15] roxygen_0.1-3             digest_0.5.0             
[17] codetools_0.2-8           haselst_0.1              
[19] blat_0.1                  genomics_0.1             
[21] mjcbase_0.1               GEOquery_2.19.2          
[23] cor_0.1                   xtable_1.5-6             
[25] rgl_0.92.798              qvalue_1.26.0            
[27] igraph_0.5.5-2            graph_1.30.0             
[29] XML_3.4-2                 SparseM_0.89             
[31] Biobase_2.12.2            sos_1.3-1                
[33] brew_1.0-6                gplots_2.8.0             
[35] caTools_1.12              bitops_1.0-4.1          
[37] gdata_2.8.1               gtools_2.6.2             

loaded via a namespace (and not attached):
 [1] affy_1.30.0           affyio_1.20.0         annotate_1.30.0      
 [4] hdrcde_2.15           KernSmooth_2.23-6     lattice_0.19-30      
 [7] MASS_7.3-13           Matrix_0.999375-50    methylumi_1.8.0      
[10] mgcv_1.7-6            nlme_3.1-101          preprocessCore_1.14.0
[13] RCurl_1.6-7           tcltk_2.13.1          tools_2.13.1         


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