Hii everyone,

I have 20 samples with Illumina Mouse-Ref 8 V2 microarray chips, and output from GenomeStudio as two files for each samples:

• named with sample_beadTypeFile.txt (header as Illumicode + N + Mean.GRN + Dev.GRN)
• named with sample_perBeadFile.txt (header as Code + Grn)

I aim to summarize the data into a format with headers: Illumicode, mean.Grn (for each sample), and detection p-value. However, my attempts using the beadarray and lumi R packages have not been successful.

I already read all _beadTypeFile.txt in list with read.table or BeadSetIllumina(storageMode: list)with readbeadMSV, but not sure how to integrate all samples with Probe_Id, sample_ID, Detection Pval. Thanks a lot for your suggestions and ideas!

Best regards, Na

GenomeStudio produces IDAT files that you can read using the read.idat function in limma. That is the recommended way to read GenomeStudio output.

Alternatively, GenomeStudio has an option to export all the data into a text file with column headings "Probe_Id, sample_ID, Detection Pval" etc, which can be read into limma using the read.ilmn function.

I do not think that you can create either the IDAT files or the export summary from the two files that you mention. I don't know of a way to process those files yourself. I don't think you should be dealing with perBead files at all, to be honest.