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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