[BioC] read.ilmn in limma 3.18.10

[Scott Christley]

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