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

[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 4.3 years ago by gokcen.eraslan10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 179 users visited in the last hour