Hi Leon, I guess the problem was caused by the mismatch between the column names of control probe data and expression data. Can you send me the return of sessionInfo() and the code of adding control data to the LumiBatch object? It will be helpful for me to find the problem. Thanks! Pan On 10/23/08 1:53 AM, "Leon Peshkin" <pesha at="" hms.harvard.edu=""> wrote: > Dear Pan, > I was wondering if you could help me resolve the issue with lumi > package, > I am able to load Illumina data with lumiR, but then when I try > background adjustment > it fails: > > A0 <- lumiR("killme.txt", convertNuID =FALSE, inputAnnotation =FALSE) >> B0 <- lumiB(A0,method='bgAdjust') > Error in `[.data.frame`(control, , sampleNames(lumiBatch)) : > undefined columns selected > > > > -Leon > > > Dr. Leon Peshkin, Senior Research Scientist > Systems Biology Dept., Longwood Av. 200 > Harvard Medical School, Boston, MA 02115 > tel: (617) 432-5483 >