[BioC] Quality Images Website moved

David Ruau druau at ukaachen.de
Thu Nov 17 19:26:12 CET 2005

Thanks for your answer!
Another question more the community in general:
Do you think we can ask Affymetrix to send us another chip when we do 
have a considerable artifact which is only visible with the help of the 
false color image?
Here we already did that when the chip was having a visible scratch on 
the scan picture (= the regular one in B&W).


On Nov 17, 2005, at 17:46, Ben Bolstad wrote:

> 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 
> 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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