On Dec 17, 2007 5:28 PM, Jakub Mieczkowski <kubamieczkowski@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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