Hi Nolwenn, The crlmm package should be able to handle your 610k quad data. You'll need idat files rather than bead-level text files to get started. Take a look at the crlmmIllumina vignette for further information BTW, the human610quadv1bCrlmm package is a chip-specific package which contains parameters used internally by crlmm - it isn't really an annotation package. I hope this helps. Best wishes, Matt > I think the annotation package you want is human610quadv1bCrlmm which > works with the crlmm package. > > beadarray doesn't support SNP arrays very well at the moment although > we plan to do something about that for future releases. > > Best, > > Mark > > On Wed, Apr 28, 2010 at 5:13 PM, Nolwenn Le Meur <nlemeur at="" irisa.fr=""> wrote: >> Hi everyone, >> >> I am trying to analyse illumina SNP array for GWAS but (as many of you) >> I >> have annotation problems. >> The experiment files are not recent and the chip type is >> ?Human610-Quadv1_B. >> ?Does that correspond to the illuminaHumanv1.db for annotation? >> >> I have tried to use the Humanv1 annotation with the readIllumina() >> function >> of the beadarray package but it seems not to be recognized by the next >> functions I use in my analysis (e.g. createBeadSummaryData) >> >> Here is for example the header of one of my txt files with measurements >> : >> >> Code ? ?Grn ? ? GrnX ? ?GrnY ? ?Red ? ? RedX ? ?RedY >> 10600301 ? ? ? ?2850 ? ?886.7655 ? ? ? ?7162.112 ? ? ? ?2645 ? ?901.0966 >> ? ?7157.959 >> 10600301 ? ? ? ?2256 ? ?1402.927 ? ? ? ?1904.34 2426 ? ?1417.054 >> ?1900.684 >> 10600301 ? ? ? ?2425 ? ?1112.202 ? ? ? ?5480.152 ? ? ? ?2405 ? ?1126.806 >> ? ?5476.067 >> >> and the annotation file I have in hand (also txt) >> >> Human610-Quadv1_B.bpm.Address ? Name ? ?Chr ? ? Position >> 10600301 ? ? ? ?rs10000010 ? ? ?4 ? ? ? 21227772 >> 10600305 ? ? ? ?rs10006395 ? ? ?4 ? ? ? 6913032 >> 10600309 ? ? ? ?rs10006554 ? ? ?4 ? ? ? 168208659 >> >> Any help is appreciated. >> >> Nolwenn Le Meur >> >> IRISA Symbiose D151 >> Universit? de Rennes I >> Campus Beaulieu >> 35042 Rennes Cedex >> France >> Phone: +33 2 99 84 71 17 >> Fax: +33 2 99 84 71 71 >> E-mail: nlemeur at irisa.fr >> Web: http://www.irisa.fr/symbiose/nolwenn_le_meur ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}