I have followed the instructions in this thread https://stat.ethz.ch/pipermail/bioconductor/2008-November/025282.html apart from using GenomeStudio to read in Illumina Human Cyto SNP-12 Bead Chip data. But when trying to read in the files I get the following error: mydata<-read.SnpSetIllumina(Sample_Map2Samplesheet("Sample_Map.txt"),r eportfile="FinalReport.txt") Error in read.SnpSetIllumina(Sample_Map2Samplesheet("Sample_Map.txt"), : subscript out of bounds The error occurs when running line: G <- G[, selected] content of variable "selected": [1] "sentrix_id_4554318341_R01C01" "sentrix_id_4554318341_R01C02" [3] "sentrix_id_4554318341_R02C01" "sentrix_id_4554318341_R02C02" [5] "sentrix_id_4554318341_R03C01" "sentrix_id_4554318341_R03C02" [7] "sentrix_id_4554318341_R04C01" "sentrix_id_4554318341_R04C02" [9] "sentrix_id_4554318341_R05C01" "sentrix_id_4554318341_R05C02" [11] "sentrix_id_4554318341_R06C01" "sentrix_id_4554318341_R06C02" G[1:3,] 4554318341_R01C01 4554318341_R01C02 4554318341_R02C01 cnvi0111185 1416 917 1418 cnvi0111186 7080 6714 7680 cnvi0111187 982 773 1216 4554318341_R02C02 4554318341_R03C01 4554318341_R03C02 cnvi0111185 1166 1343 1200 cnvi0111186 7465 7158 8150 cnvi0111187 1016 1075 997 4554318341_R04C01 4554318341_R04C02 4554318341_R05C01 cnvi0111185 1445 1169 1485 cnvi0111186 8428 8732 8995 cnvi0111187 983 1005 1246 4554318341_R05C02 4554318341_R06C01 4554318341_R06C02 cnvi0111185 1819 1269 1449 cnvi0111186 8702 5399 4641 cnvi0111187 1317 1314 1183 I think I miss something in the input files: Sample_map.txt (Group, Parent1, Parent2 and Replicate are empty): Index Name ID Gender Plate Well Group Parent1 Parent2 Replicate SentrixPosition 1 07-019117 4554318341_R01C01 Unknown WG9999912-DNA A01 4554318341_R01C01 2 08-001712 4554318341_R01C02 Unknown WG9999912-DNA D01 4554318341_R01C02 3 07-007836 4554318341_R02C01 Unknown WG9999912-DNA G01 4554318341_R02C01 4 06-013382 4554318341_R02C02 Unknown WG9999912-DNA B02 4554318341_R02C02 5 06-008925 4554318341_R03C01 Unknown WG9999912-DNA B01 4554318341_R03C01 6 06-006744 4554318341_R03C02 Unknown WG9999912-DNA E01 4554318341_R03C02 7 07-020190 4554318341_R04C01 Unknown WG9999912-DNA H01 4554318341_R04C01 8 NA10859_1 4554318341_R04C02 Unknown WG9999912-DNA C02 4554318341_R04C02 9 08-000591 4554318341_R05C01 Unknown WG9999912-DNA C01 4554318341_R05C01 10 07-015573 4554318341_R05C02 Unknown WG9999912-DNA F01 4554318341_R05C02 11 08-004776 4554318341_R06C01 Unknown WG9999912-DNA A02 4554318341_R06C01 12 NA10859_2 4554318341_R06C02 Unknown WG9999912-DNA D02 4554318341_R06C02 The output created by Sample_Map2Samplesheet: [Header] Investigator Name, Project Name, Experiment Name, Date, [Data] Index,Sample_Name,ID,Gender,Sample_Plate,Well,Group,Parent1,Parent2,Re plicate,Sentrix_Position,Pool_ID,Sentrix_ID 1,07-019117,4554318341_R01C01,Unknown,WG9999912-DNA,A01,,,,,4554318341 _R01C01,pool_id,sentrix_id 2,08-001712,4554318341_R01C02,Unknown,WG9999912-DNA,D01,,,,,4554318341 _R01C02,pool_id,sentrix_id 3,07-007836,4554318341_R02C01,Unknown,WG9999912-DNA,G01,,,,,4554318341 _R02C01,pool_id,sentrix_id 4,06-013382,4554318341_R02C02,Unknown,WG9999912-DNA,B02,,,,,4554318341 _R02C02,pool_id,sentrix_id 5,06-008925,4554318341_R03C01,Unknown,WG9999912-DNA,B01,,,,,4554318341 _R03C01,pool_id,sentrix_id 6,06-006744,4554318341_R03C02,Unknown,WG9999912-DNA,E01,,,,,4554318341 _R03C02,pool_id,sentrix_id 7,07-020190,4554318341_R04C01,Unknown,WG9999912-DNA,H01,,,,,4554318341 _R04C01,pool_id,sentrix_id 8,NA10859_1,4554318341_R04C02,Unknown,WG9999912-DNA,C02,,,,,4554318341 _R04C02,pool_id,sentrix_id 9,08-000591,4554318341_R05C01,Unknown,WG9999912-DNA,C01,,,,,4554318341 _R05C01,pool_id,sentrix_id 10,07-015573,4554318341_R05C02,Unknown,WG9999912-DNA,F01,,,,,455431834 1_R05C02,pool_id,sentrix_id 11,08-004776,4554318341_R06C01,Unknown,WG9999912-DNA,A02,,,,,455431834 1_R06C01,pool_id,sentrix_id 12,NA10859_2,4554318341_R06C02,Unknown,WG9999912-DNA,D02,,,,,455431834 1_R06C02,pool_id,sentrix_id In advance, many thanks. Christian