hi kripa, You haven't mentioned what BioC package you are using. I'm guessing it to be *lumi. *You should export out *Sample Probe profile* Also using the *nuID* functionality is optional. You may skip that for your initial analysis. What exactly you want to do in R/ BioC. There are two packages in BioC: * beadarray* & *lumi*. The former is if for starting analysis from image files (It has an alternative background correction algorithm). The latter is if you prefer to do background correction in BeadStudio rather then normalization and differential expression in BioC. To start you off, this is to read in the BeadStudio out file - x.lumi<-lumiR(fileName="YOUR_FILE_NAME_EXPORTED_FROM_BEADSTUDIO.txt",sep="\t",detectionTh=0.01,na.rm=TRUE,convertNuID=FALSE,lib.mapping=NULL,dec='.',parseColumnName=TRUE,checkDupId=TRUE,QC=TRUE,columnNameGrepPattern=list(exprs='AVG_Signal',se.exprs='BEAD_STDERR',detection='Detection Pval',beadNum='Avg_NBEADS'),inputAnnotation=TRUE,annotationColumn=c('ACCESSION','SYMBOL','PROBE_START','CHROMOSOME','PROBE_CHR_ORIENTATION','PROBE_COORDINATES','DEFINITION'),verbose=TRUE) Refer to this for details. The pdf is quite illustrative - http://www.bioconductor.org/packages/2.7/bioc/vignettes/lumi/inst/doc/lumi.pdf You may choose to keep inputAnnotation=FALSE instead. cheers, amit m Graduate Student IGIB, Delhi On Wed, Mar 23, 2011 at 2:45 AM, Kripa R wrote: > > Hi everyone! > > I've just obtained data from illumina HT12 chips and > have taken a preliminary look at the data in genomestudio. I'd like to > do further analysis in R but I'm having trouble creating the batch file. > I've exported the Group_Probe_Profile.txt sheet but when using this I > get errors regarding lack of nuID and such. Does anyone have familiarity > with doing this; are there other files I'm missing? > > Some guidance would be greatly appreciated! > > Thanks, > > .kripa > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- --------------------------------------------------------------- The robbed that smiles, steals something from the thief. - Shakespeare --------------------------------------------------------------- [[alternative HTML version deleted]]