[BioC] different density

[Naomi Altman]

A plot that is often quite informative is log(exprs) vs log(exprs) 
for the unnormalized probes from replicate arrays (or just log(pm) vs 
log(pm)) .  If the arrays are "good" the technical replicates have 
high correlation and are tightly clustered on the diagonal of this 
plot, and biological replicates are shaped more like an American 
football - not a bit more pointy at the extremes than an ellipse.

Bad arrays are either much more scattered, do not show a diagonal 
trend or may be jammed into the upper or lower section of the plot.

--Naomi


At 05:30 PM 12/18/2007, Jakub Mieczkowski wrote:
>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
> >
> >
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
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