[BioC] kooperberg correction

[Matthew Ritchie]

Hi Jason,

> Hi
>
> using R 1.8.0
> limma 1.5.1
>
> Attempting to use the Kooperberg background correction in Limma
>  > RGmodel <- kooperberg(FILES, layout=LAYOUT, fg="mean", bg="mean")
>
> &
>
>  > RGmodel <- kooperberg(FILES, layout=LAYOUT, fg="median", bg="median")
>
> both return following error:
>
>
> Error in integrate(.numeratorBayesianAdjustedFG, ifelse((fg - bg - 4 *
> :
>     a limit is missing

This means that one of the limits (lower/upper) passed to the function
integrate() is a missing value (NA) for one of the genes.  I wouldn't have
expected this error because the limits are calculated using data from the
GenePix results files without logging.

Can you check that the columns "F532 Mean", "F532 SD", "B532 Mean", "B532
SD", "F635 Mean", "F635 SD", "B635 Mean", "B635 SD", "F Pixels" and "B
Pixels" in your files don't have any missing values?

If there are no NA's, perhaps you can send me an example of one of your
.gpr files so I can take a closer look at the problem.  Best wishes,

Matt Ritchie

> any ideas much appreciated
>
> thanks
>
> Jason