Read Illumina Iscan Data Directly Into R Using Beadarraymsv

Question

[John Clark]

Hi guys

I was trying to read illumina iscan data into the package "beadarrayMSV". I could not figure out what is proper way to do so..

There are bunch of files in the chip directory, I could not locate summary file.

The folder output from the iscan data has the following files:

07/21/2011  02:20 PM    <DIR>          .
07/21/2011  02:20 PM    <DIR>          ..
03/15/2011  12:14 PM            24,586 5891957032.sdf
05/17/2011  03:45 PM            21,831 5891957032_qc.txt
05/17/2011  03:12 PM         2,077,270 5891957032_R01C01_1-Swath1_Grn.jpg
05/17/2011  03:12 PM         2,004,197 5891957032_R01C01_1-Swath1_Red.jpg
05/17/2011  03:12 PM             1,353 5891957032_R01C01_1.xml
05/17/2011  03:12 PM            75,091 5891957032_R01C01_Grn.idat
05/17/2011  03:12 PM            75,091 5891957032_R01C01_Red.idat
05/17/2011  03:16 PM         2,040,807 5891957032_R01C02_1-Swath1_Grn.jpg
05/17/2011  03:16 PM         1,992,992 5891957032_R01C02_1-Swath1_Red.jpg
05/17/2011  03:16 PM             1,351 5891957032_R01C02_1.xml
05/17/2011  03:16 PM            75,091 5891957032_R01C02_Grn.idat
05/17/2011  03:16 PM            75,091 5891957032_R01C02_Red.idat
05/17/2011  03:13 PM         2,115,222 5891957032_R02C01_1-Swath1_Grn.jpg
05/17/2011  03:13 PM         1,986,481 5891957032_R02C01_1-Swath1_Red.jpg
05/17/2011  03:13 PM             1,351 5891957032_R02C01_1.xml
05/17/2011  03:13 PM            75,090 5891957032_R02C01_Grn.idat
05/17/2011  03:13 PM            75,090 5891957032_R02C01_Red.idat
05/17/2011  03:16 PM         2,081,163 5891957032_02C02_1-Swath1_Grn.jpg
05/17/2011  03:16 PM         2,008,217 5891957032_02C02_1-Swath1_Red.jpg
05/17/2011  03:16 PM             1,352 5891957032_02C02_1.xml
05/17/2011  03:16 PM            75,090 5891957032_02C02_Grn.idat
05/17/2011  03:16 PM            75,090 5891957032_02C02_Red.idat
.......
05/17/2011  03:15 PM         2,156,167 5891957032_R10C01_1-Swath1_Grn.jpg
05/17/2011  03:15 PM         2,064,695 5891957032_R10C01_1-Swath1_Red.jpg
05/17/2011  03:15 PM             1,353 5891957032_R10C01_1.xml
05/17/2011  03:15 PM            75,091 5891957032_R10C01_Grn.idat
05/17/2011  03:15 PM            75,091 5891957032_R10C01_Red.idat
05/17/2011  03:19 PM         2,052,442 5891957032_R10C02_1-Swath1_Grn.jpg
05/17/2011  03:19 PM         2,016,106 5891957032_R10C02_1-Swath1_Red.jpg
05/17/2011  03:19 PM             1,351 5891957032_R10C02_1.xml
05/17/2011  03:19 PM            75,091 5891957032_R10C02_Grn.idat
05/17/2011  03:19 PM            75,091 5891957032_R10C02_Red.idat
05/17/2011  03:15 PM         2,094,697 5891957032_R11C01_1-Swath1_Grn.jpg
05/17/2011  03:15 PM         2,056,090 5891957032_R11C01_1-Swath1_Red.jpg
05/17/2011  03:15 PM             1,351 5891957032_R11C01_1.xml
05/17/2011  03:15 PM            75,091 5891957032_R11C01_Grn.idat
05/17/2011  03:15 PM            75,091 5891957032_R11C01_Red.idat
05/17/2011  03:19 PM         2,111,930 5891957032_R11C02_1-Swath1_Grn.jpg
05/17/2011  03:19 PM         2,034,800 5891957012_R11C02_1-Swath1_Red.jpg
05/17/2011  03:19 PM             1,351 5891957032_R11C02_1.xml
05/17/2011  03:19 PM            75,091 5891957032_R11C02_Grn.idat
05/17/2011  03:19 PM            75,091 5891957032_R11C02_Red.idat
05/17/2011  03:16 PM         2,022,309 5891957032_R12C01_1-Swath1_Grn.jpg
05/17/2011  03:16 PM         2,052,498 5891957032_R12C01_1-Swath1_Red.jpg
05/17/2011  03:16 PM             1,351 5891957032_R12C01_1.xml
05/17/2011  03:16 PM            75,091 5891957032_R12C01_Grn.idat
05/17/2011  03:16 PM            75,091 5891957032_R12C01_Red.idat
05/17/2011  03:19 PM         2,105,529 5891957032_R12C02_1-Swath1_Grn.jpg
05/17/2011  03:19 PM         2,036,380 5891957032_R12C02_1-Swath1_Red.jpg
05/17/2011  03:19 PM             1,352 5891957032_R12C02_1.xml
05/17/2011  03:19 PM            75,091 5891957032_R12C02_Grn.idat
05/17/2011  03:19 PM            75,091 5891957032_R12C02_Red.idat
05/17/2011  02:24 PM            63,419 Effective.cf
05/17/2011  03:19 PM             2,387 Metrics.txt

I am new to this, you help is highly appreciated

Edits: beadarrayMSV is supposed to have has similar functionality as beadarray package according to documentation.

[Sean Davis]

I would suggest writing to the author of the package.

[John Clark]

THANK YOU FOR SUGESTION..I emailed the author...if I get any answer from the author I will post the correct answer to benifit of the community ..

Answer 1

[Lars Gidskehaug]

The function readBeadSummaryOutput() requires that the scanner protocol has been set to save bead summary data in the following format:

Illumicode,N,Mean GRN,Dev GRN,Mean RED,Dev RED

10040,20,5565,1252,250,89

10128,29,247,114,719,199

10193,32,7657,1811,5432,943

10343,34,12462,2707,367,165

10360,35,626,136,12449,1610

...etc

N is number of beads and Mean and Dev are robust means and standard deviations of the individual channel intensities. If the scanner has not been set to produce such summary files, the bioconductor package beadarray can be used to create the files. For more examples of data file formats, please have a look in the extdata directory of the installation folder, which contains different xz-compressed files.

Good luck!