Question: Error in the Illumina ID to Gene Symbol mapping through lumi package
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gravatar for gokcen.eraslan
3.9 years ago by
Germany
gokcen.eraslan10 wrote:

I am using lumi package to map some Illumina probe IDs to gene symbols but I get the following output. It seems some entries are shifted somehow. Is this a bug in the package?

 

> probeID2nuID(c("ILMN_1798177", "ILMN_1798177", "ILMN_1753164", "ILMN_1753164"), 
lib.mapping = 'lumiHumanIDMapping', 
chipVersion = 'HumanRef8_V3_0_R3_11282963_A')

             Search_Key   ILMN_Gene     Accession      Symbol               Probe_Id      Array_Address_Id nuID                
ILMN_1798177 "ILMN_27265" "NM_145165.2" "ILMN_1798177" "3lQi3D.M5XlDtdNz5I" "CHURC1"      "CHURC1"         "0006370612"        
ILMN_1798177 "CHURC1"     "CHURC1"      "0006370612"   "ILMN_27265"         "NM_145165.2" "ILMN_1798177"   "3lQi3D.M5XlDtdNz5I"
ILMN_1753164 "ILMN_15237" "NM_006390.2" "ILMN_1753164" "ZXeddX1QpPgng7lB6Q" "IPO8"        "IPO8"           "0000460411"        
ILMN_1753164 "IPO8"       "IPO8"        "0000460411"   "ILMN_15237"         "NM_006390.2" "ILMN_1753164"   "ZXeddX1QpPgng7lB6Q"
 
 

Here is my sessionInfo():

> sessionInfo()

R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Antergos

locale:
[1] LC_CTYPE=en_DK.UTF-8       LC_NUMERIC=C               LC_TIME=en_DK.UTF-8        LC_COLLATE=en_DK.UTF-8     LC_MONETARY=en_DK.UTF-8    LC_MESSAGES=en_DK.UTF-8 
[7] LC_PAPER=en_DK.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_DK.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] annotate_1.46.0           XML_3.98-1.3              lumiHumanIDMapping_1.10.0 RSQLite_1.0.0             DBI_0.3.1                 AnnotationDbi_1.30.1    
[7] GenomeInfoDb_1.4.1        IRanges_2.2.5             S4Vectors_0.6.1           lumi_2.20.2               Biobase_2.28.0            BiocGenerics_0.14.0      
ADD COMMENTlink written 3.9 years ago by gokcen.eraslan10
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