[BioC] Quality Images Website moved

[Ben Bolstad]

Hi David,

To actually decide whether or not to remove a chip from a dataset the
recommended method is to use either or both of the RLE and NUSE boxplots
and look for arrays with boxes that are centered higher or more spread
than the others.

The chip pseudo-images give you the ability to potentially diagnose the
cause of the lesser quality data. Generally speaking, smaller artifacts
are not problematic (and probably aren't even reflected in the NUSE or
RLE) although they can sometimes be interesting as can be seen by some
of the images in the gallery. This is because on most modern chips the
probes making up each probeset are distributed all across the array,
which means that there is typically only one probe in any probeset
affected. Thus provided you are using a robust expression measure eg RMA
or the expression values from fitPLM itself you won't have any problem.

Larger artifacts are more problematic (and usually you'll find
correspond with NUSE and RLE) because it typically means there are some
probesets with a large number of probes being affected. If it is really
bad you probably don't have much choice but to remove the whole chip
from subsequent analysis. 

If you feel you are somewhere in between then your best option is
probably to do some down-weighting of lesser quality data. I believe if
you do your analysis using limma and supply the PLMset from fitPLM it
will do something like this, though you might have other ideas about how
to do the weighting. I think this would be a better approach then just
completely masking the area.


Thanks, 

Ben 


On Thu, 2005-11-17 at 10:32 +0100, David Ruau wrote:
> Dear Dr. Bolstad,
> 
> Thanks for those really interesting gallery, it make you feel less 
> alone when you have a look at your own chips after.
> I would like to know if a tool exist to remove the badly hybridized 
> zone of the chip from the analysis?
> I mean just keeping the good zone of the chip or do not include the bad 
> zone into the rest of the analysis.
> 
> I motivated by this problem because my boss always gnash one's teeth 
> when I say that this chip is bad and we should not use it.
> 
> David
> 
> On Nov 10, 2005, at 1:03, Ben Bolstad wrote:
> 
> > The gallery of quality images from fitPLM has moved to
> >
> > http://plmimagegallery.bmbolstad.com/
> >
> > As always, contributions are welcome.
> >
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