[BioC] beadarraySNP and GenomeStudio report file

[Christian Ruckert]

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"),reportfile="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,Replicate,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,,,,,4554318341_R05C02,pool_id,sentrix_id
11,08-004776,4554318341_R06C01,Unknown,WG9999912-DNA,A02,,,,,4554318341_R06C01,pool_id,sentrix_id
12,NA10859_2,4554318341_R06C02,Unknown,WG9999912-DNA,D02,,,,,4554318341_R06C02,pool_id,sentrix_id


In advance, many thanks.

Christian