[BioC] AffyPLM

[Matthew Hannah]

Lawrence,

In my experience of using the images its very easy to see artefacts such
as dirt or air bubbles as these show up as green on the images. Recently
I also detected a green strip across a certain batch of chips and I'm 
currently looking into whether there could be a scanner problem. Also a
'bad' chip could appear darker overall. Ideally I guess you're looking for
a random distribution of colours on a chip and a similar overall colour
between chips. In general chips that look quite bad still seem to give
resonable data, I don't know what the point is when you exclude a chip.

As for the residuals vs. SE perhaps this poster might help.

http://stat-www.berkeley.edu/users/terry/Group/talks/Aug2003/QCPoster.pdf

As a secondary point is the NUSE discussed in the poster the same as the 
model SE that you can boxplot in affyPLM, as the boxplots are adjusted so 
each probeset has a median of 1?

I'd also appreciate a lay-mans explanation of what the output of PLM and
what it can be used for. For example can the SE's be used in any way to 
get some kind of confidence for differential expression?

Cheers,
Matt