[BioC] Quality of Affy Chips with the affy package

Laurent Gautier laurent@cbs.dtu.dk
Fri, 14 Feb 2003 03:38:37 +0100

On Thu, Feb 13, 2003 at 05:58:39PM +0100, Oliver Hartmann wrote:
> Dear list members,
> in chapter 4 of "Textual description of affy" several methods for 
> quality control are described: hist(), image(), boxplot() and RNA 
> degradation plots.
> Has anybody used these methods to identify bad quality chips? When do 
> you exclude a chip from further analysis? What's your decision rule?
> Any other suggestions on how to identify bad quality from the data alone?

'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).

Few other things are being worked on...

About the decision rule, I thought it was a function of parameters 'cost',
'deadline', 'availability of samples' and 'results'. ;)