Dear Mondher, I'd suggest you try using beadarraySNP. The beadarray package doesn't currently support BeadStudio output from Illumina's genotyping arrays. It will read in BeadStudio output from Illumina's expression arrays, and can handle raw bead-level data (text files and tiffs) for single-channel (expression) and two-colour (genotyping and methylation) BeadArrays. Best wishes, Matt > Mondher > > For CNV analysis you might also want to look at the beadarraySNP package, and > the paper cited in the vignette for beadarraySNP. > > Richard. > > Herve Pages wrote: >> Hi Mondher, >> >> A good start is to read the documentation available in the package. >> For example you can download the PDF files available on this page: >> >> http://bioconductor.org/packages/2.3/bioc/html/beadarray.html >> >> or open them directly from your R session with openVignette() (after you've >> managed to install and load the package). We call these documents >> vignettes: >> they generally contain examples (with code) on how to use the package. They >> are a great way to learn how to use it. Then when it's time to dive into >> the gory details of how to use a particular function, '?somefuntion' >> is your friend, especially the example section. >> >> Ask here again if you have a more specific questions about the package. >> >> Good reading! >> H. >> >> >> Mondher GATRI wrote: >>> Dear All, >>> >>> I'm Mondher Gatri, I'm working at EPFL, Switzerland. during my work >>> I'm dealing with SNPs datasets. I would like to use BeadArray to >>> normalize BeatStudio SNPs data. Would you please inform me about how >>> to use beadarray package for normalization, quality control and CNV >>> computing. >>> >>> Kink regards, >>> Mondher This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.