[BioC] different density

[Jakub Mieczkowski]

First of all thank you very much for response.
Unfortunately I don't understand what do you mean that I should look 
closely. I've got only .CEL files and I have no idea what else I can do. 
QCReport is available here:

http://students.mimuw.edu.pl/%7Ejm214641/AffyQCReport.pdf

On RLE and RNAdeg plots I can't distinguish 4 "outliers" from rest.

How can I check what was measured (background or signal)? Should I use 
P/M/A method or something different? Are there any other Quality Control 
methods than QCReport, RLE, NUSE and image analysis (residuals, 
weigths). Maybe, in this situation, some pre-processing methods are 
better than another? Maybe linear transformation can help?
Thank You,
Kuba

Sean Davis pisze:
> 
> 
> On Dec 17, 2007 5:28 PM, Jakub Mieczkowski <kubamieczkowski at op.pl 
> <mailto:kubamieczkowski at op.pl>> wrote:
> 
>     Hi All,
>     I'm new to Bioconductor and I want to analyse time course data (6 time
>     points, 3 oligo arrays in each). During the quality control (QCReport) I
>     found that 4 arrays have different densities. What is shown here:
> 
>     http://students.mimuw.edu.pl/~jm214641/BoxANDden.pdf
>     <http://students.mimuw.edu.pl/%7Ejm214641/BoxANDden.pdf>
> 
>     Plot of NUSE shows differences too. Images of weights are a little bit
>     different form rest, but I can't notice any artefacts.
>     3 of them, are from the same time point.
> 
>     Should I remove them from further analysis (differences can have
>     biological basis)? Or maybe I just can't use methods like RMA (because
>     of different distributions)? Do you have any suggestions?
> 
> 
> Hi, Kuba.  You will probably need to look closely at the QC information 
> on these arrays, but I would be concerned that these arrays didn't work 
> for one reason or another given the much lower intensities associate 
> with your four "outlier arrays".  I do not think I would blindly apply 
> RMA to those arrays without getting a better sense of whether or not 
> they are measuring something and not just representing mostly background 
> signal.
> 
> Sean
> 
>