[BioC] Cel image

[Henrik Bengtsson]

Hi,

it all depends.  There are at least two ways to generate spatial plots
of an microarray.  The first one is to plot the probe intensities,
which you get directly from the CEL file(s).  Here you want to pick
some color transform (e.g. sqrt or log) and color map.  This might
give some clues/hints on extreme spatial artifacts.  If you fit
probe-level models to the units ("probesets"), you can plot the PLM
residuals as well, because that will better show you the spatial
artifacts compare with looking at the probe intensities.

( BTW, be careful when you look at spatial intensity plots on the
screen, especially when you zoom in and out, because you will most
likely get rastering effects that are due to the display and that are
not in the array. Some illustrations I found by a quick search:
http://pixelmapping.wikispaces.com/Pixel+mapping+explained )

Depending on what chip type and type of analysis you are looking
at/using, a spatial artifact has more or less severe impact on the end
result.  For instance, if you run standard gene expression arrays
where each unit has multiple probes, a spatial artifact is less severe
than if you run, say tiling arrays or single-probe copy-number arrays.
 In the former case, two things typically save/help you: i) the fact
that Affymetrix randomized the position of the probes such that
spatial artifacts are likely only to affect one or two probes in a
unit, and ii) robust fitting of probe-level models (PLM, e.g.
log-additive modelling via via affyPLM).
However, in the latter case with single-probe units, neither will help
you.  Maybe some downstream algorithm has some robustification to it,
that you have to check out.

So, if you are trying to identify poor hybridizations from spatial
images and decide which ones to filter out, your filtering criteria
really depend on the chip type and what it is going to be used for.

Cheers

Henrik


On 9/20/07, Yogi Sundaravadanam <yogi.sundaravadanam at agrf.org.au> wrote:
> Thanks for the reply... let me rephrase that a bit.  I would like to know as to how I should interpret the image.
>
> Cheers
> Yogi
>
>  -----Original Message-----
> From: smohapat at vbi.vt.edu [mailto:smohapat at vbi.vt.edu]
> Sent: Friday, 21 September 2007 10:46 AM
> To: Yogi Sundaravadanam
> Cc: bioconductor
> Subject: Re: [BioC] Cel image
>
> Hi Yogi:
>
> > How informative can these images be? In other words, just be looking at
> > the images, would I be able to pick out chips that aren't OK?
> >
>
> I usually run some other checks with simpleaffy and affyPLM before
> considering a chip of poor quality.
>
> -- Saroj
>
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