Hi Henrik, Thanks for your answer.

>  It might be that you ran out of
> memory (the you got an error message).  If you used cut'n'paste,
> instead of source(), to do the analysis, it might be that one of the
> fit() methods was preemptively finished.  If so, not all units have
> been fitted.  Rerun with ram=1 to see if you get a different result;
> the units already fitted will be skipped.

The memory was not an issue, I did not get any errors doing copy and
paste of the code, and results remained the same after using ram=1. I
used 500 since I have a 32GB machine.

> I'm also not sure if
> > 431210/(1190297*107)
> [1] 0.003385710
> is an exceptionally large fraction.  

Agree that this is not a large fraction, I just want to be sure that
this does not happen to the most interesting exons :)

>Note also that 431210/107 is
> exactly 4030; it could be that it is the exact same 4030 units that
> are NA in all samples.

Yes, maybe I should mention that the NaN values occur for all samples.
The group value is 1 for all these 4030 probes with NaN values.

Also, the Inf values occur for all samples for 8 probes (various units
and groups).

        unit group   cell 001_R887 002_R779 003_R649
144265  3731   237 144265      Inf      Inf      Inf
179089  4631   149 179089      Inf      Inf      Inf
180652  4652   234 180652      Inf      Inf      Inf
193136  5020   183 193136      Inf      Inf      Inf
204140  5335   145 204140      Inf      Inf      Inf
269865  7329   135 269865      Inf      Inf      Inf
306336  8509   364 306336      Inf      Inf      Inf
513819 16550   132 513819      Inf      Inf      Inf


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