[BioC] marray and gathering additional information from GenePix GPR file

[Daniel Brewer]

Jenny Drnevich wrote:
> Hi Daniel,
> 
> 
> First, I would caution you about discarding all spots called 'bad' by
> your GenePix setup - do you really know what it's doing? Often, spots
> are labeled 'bad' if the spot foreground is not detectable above some
> level of the background. Unless there is a defect on the chip, these
> type of spots are actually 'real' data, not 'bad' data - more like a
> value of 0. Now, the number that is associated with that spot is not
> entirely accurate, but it is relatively accurate compared to spots with
> detectable values. In an extreme example, by throwing out these spots,
> you may not detect a gene that is only turned on in one of your
> treatment groups! However, you do need to discard spot values that are a
> result of obvious defects on the array, so you still need an answer to
> your question:
> 

Thanks for that, that makes a lot of sense.  There are "spots" that are
empty by design (there is no spot there) and are indicated as such in
maControls. Is it ok, and sensible to remove these from the object?
i.e.
> mraw2 <- mraw2[maControls(mraw2) == 'probes']

Thanks

Daniel