[BioC] Quality of Affy Chips with the affy package

[Hinnerk Boriss]

> 'image' lets you do a visual inspection of the chip 
> (scratches, air bubble(s),
> washing step problem, ..., should be visible).
> 'hist' can let you see saturation (if you have the 
> distribution of probe
> intensities showing a strange 'bump' on the higher end of the 
> intensity range,
> you may suspect that the captor (a CCD camera I believe) get too much
> an cut off the signal. You can confirm with a scatter plot (or matrix
> of scatter plots (see pairs.AffyBatch))).
> 'boxplot' and 'hist' can let you vizualize the effect of normalization
> for example (quality control on the processing step).
>

Hi,

if I find such areas with scratches, bubbles or saturation on a chip,
how can I mask them? 

Also, if probe level intensities go into saturation, how does that
affect signal values? I ask, because there will generally be probes in a
probe set that won't have that problem. Sure, this will depend on the
signal value estimation method. How do RMA and MBEI react when some
probes ru in saturation?

Best,
Hinnerk