Hi, John You haven't really provided enough information for us to help you. The sessionInfo() would be useful so that we know what version of R and other packages you are using. A reproducible example would be great, but barring that, more information about your data (the flowSet, and flowFrames) like the output of summary() or print(), helps us to understand what the input data looks like. Calling traceback() after the error is thrown can also help tell you, and us more precisely where the error occured. If I had to make a guess, and that's all I can do given the information you've provided, I'd say look at the parameter names in your flowFrames. Sometimes R will substitute a '.' for the '-' character in parameter names. Greg Finak, Ph.D Post-doctoral Fellow Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA On 2012-02-16, at 3:06 AM, "bioconductor-request at r-project.org" <bioconductor-request at="" r-project.org=""> wrote: > Hello, > > I've been running into some issues in computing the spillover matrix using > flowCore. I've searched the archives, and there seems to be someone else > from 2 years ago who had this problem; however, I tried the suggested fixes > to no avail, and I'm not sure if the original poster ever resolved the > problem. > > Here is a brief description of my dataset: > > I have a flowSet with 10 experiments, the first of which is my unstained > control fcs file. Experiments 2-10 correspond to FITC-A PE-A PE- Cy7-A > V450-A APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A > > The following are the column names of each flowFrame: > FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A APC-A Alexa 700-A > QDot 655-A APC-Cy7-A Pac Orange-A Time > > I call the spillover function as follows: > > namepatt <- "FITC-A|PE-A|PE-Cy7-A|V450-A|APC-A|Alexa 700-A|QDot > 655-A|APC-Cy7-A|Pac Orange-A" > comp.mat <- spillover(compdat[,c(1,3,5:13)],unstained = > sampleNames(compdat)[1], patt = namepatt,fsc = "FSC-A", ssc = > "SSC-A",method = "median",useNormFilt = TRUE) > > Notice the useNormFilt = TRUE. I have set it to FALSE and also get the same > error message: Error in .local(x, ...) : subscript out of bounds > > Does anyone know what is going on here? Help is much appreciated > > Thanks, > John