Error in the Illumina ID to Gene Symbol mapping through lumi package
0
0
Entering edit mode
@gokceneraslan-8533
Last seen 7.7 years ago
Germany

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      
lumi illuminahumanv3 lumihumanidmapping • 1.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 687 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6