Hello, There seems to be a problem with read.ilmn() with the new version of limma. When trying to read the control file, there is an error that row names are not unique. x <- read.ilmn(files="probe-profile.txt", ctrlfiles="JAlverdy-JDeF- Dec2-13-ControlProbeData-FinalReport.txt", other.columns="Detection?) Error in `row.names<-.data.frame`(`*tmp*`, value = c(2900458L, 7200743L, : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ?1400044?, ?2600040?, ?6450180? I looked at the control file, and there are indeed 3 rows with the same ProbeID number. I?m not sure if that is an error or something about the specific output from BeadStudio. thanks Scott

Dear Scott, Thanks for pointing out the problem. I've fixed it today. See my reply Tim Kendall for more details. Best wishes Gordon ------- original message -------- Scott Christley schristley at uchicago.edu Tue Feb 4 18:37:23 CET 2014 Hello, There seems to be a problem with read.ilmn() with the new version of limma. When trying to read the control file, there is an error that row names are not unique. x <- read.ilmn(files="probe-profile.txt", ctrlfiles="JAlverdy-JDeF-Dec2-13-ControlProbeData-FinalReport.txt", other.columns="Detection) Error in `row.names<-.data.frame`(`*tmp*`, value = c(2900458L, 7200743L, : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': 1400044, 2600040, 6450180 I looked at the control file, and there are indeed 3 rows with the same ProbeID number. Im not sure if that is an error or something about the specific output from BeadStudio. thanks Scott ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}