[BioC] Quality of Affy Chips with the affy package

Stephen Henderson s.henderson@ucl.ac.uk
Thu, 20 Feb 2003 18:07:48 -0000

Dchip has a facility to detect outliers of a group of arrays--i.e. where the
probe pm-mm patterns don't correlate with the group. This is often due to
scratches etc..


These probesets can be exported and I imagine then used to exclude
comparisons within bioconductor.


-----Original Message-----
From: Hinnerk Boriss [mailto:boriss@izbi.uni-leipzig.de] 
Sent: Thursday, February 20, 2003 5:26 PM
To: 'Laurent Gautier'
Cc: bioconductor
Subject: RE: [BioC] Quality of Affy Chips with the affy package

> '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).


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?


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