Hi to everybody, I have started recently to analyse Illumina Bead Chip data. I started without any kind of problem and I was glad with the results until I saw that comment from the beadarray library authors: "iScan come in a different format,.... there are two images of each array section (along with two .locs files), which are labeled Swath1 and Swath2" I don't have those files, I have only the perBeadFile.txt and after the authors wrote: "Given this, simply reading the bead-level text file will result in any function that uses bead locations performing undesirably" And now I am afraid if I did something wrong.. I am not receving any message when I read my files with the function readIllumina and they have also wrote that I should receive a message from the function advising me to use processSwathData. Does anybody know in which cases using perBeadFile.txt is ok and in which cases no? thanks a lot for the help Best wishes Mireia [[alternative HTML version deleted]]

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