Hi Benbo The lumi package supports both GenomeStudio and BeadStudio output files. We recommend using probe level data, which usually is named as "Sample Probe Profile Sample.txt". There are detailed example in the lumi vignette "Using lumi: A package processing Illumina Microarray". You can download these documents at: http://www.bioconductor.org/help/bioc- views/release/bioc/html/lumi.html Also, we recommend you install R 2.12.0, so you can easily install the lumi package using biocLite('lumi') command. Tell me if you have any questions. Pan On 11/23/10 2:11 PM, "Gao, Benbo" <benbo.gao at="" joslin.harvard.edu=""> wrote: > > Dear Pan, > > Thank you for provide lumi package. I am new to R. I have data from Illumina. > But the data is output by GenomeStudio not from BeadStudio in serveral files. > I attached a piece of sample data. > Could you tell me can I use lumi package to anaylsis these kind data? How to > input the data? Do you have have some sample code I can use? > > Thank you very much. > > Benbo Gao > > Joslin Diabetes Center