Converting Behar et al. dataset from GEO to PLink format

Question

[aritra90]

Hi,

I have the Behar et al (2010) data set from GEO which is in Illumina's TOP/BOT format. It is a series matrix downloaded from GEO. They used this platform file for the Illumina genotyping BeadChip technology. In Harappa Ancestry Project page, there is a solution given to convert this data to PLink format. But, that solution is not working in my case. This script they indicate to: http://www.openbioinformatics.org/gengen/tutorial_allele_coding.html#convert_ilmnab is not running properly in my system and also, I can't understand the entire conversion process.

It would be great if anyone has done it before and help me understand the conversion procedure and if possible, the methods to do it. Looking forward to the posts.

Thanks in advance.

[h.mon]

Copy the commands you used and the errors messages. Also, copy the first few lines from the data files.