[BioC] read.ilmn in limma 3.18.10

[Gordon K Smyth]

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

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