[aroma.affymetrix] Filtering in FIRMA

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[aroma.affymetrix] Filtering in FIRMA

Marijke Van Moerbeke
Hi

I noticed that the FIRMA procedure is implemented to work on the raw .CEL files.
Is there a way to select only a specific set of units (By this I mean exons) on which FIRMA needs to be performed? And by this to leave out units that are  for example not informative?

Thanks!

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Re: [aroma.affymetrix] Filtering in FIRMA

Henrik Bengtsson-4
Hi,

the fit() method
[http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis/]
takes argument 'units', which effectively defaults to units =
seq_len(nbrOfUnits(cdf)).  If you wish to fit only a subset of the
units, you can do something like

    fit(plm, units=c(10:50, 540:800))

If you're using doFIRMA(), it is unfortunately not possible to specify
'units' this way.

Hope this helps

Henrik


On Wed, Aug 12, 2015 at 2:25 PM, Marijke Van Moerbeke
<[hidden email]> wrote:

> Hi
>
> I noticed that the FIRMA procedure is implemented to work on the raw .CEL
> files.
> Is there a way to select only a specific set of units (By this I mean exons)
> on which FIRMA needs to be performed? And by this to leave out units that
> are  for example not informative?
>
> Thanks!
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [hidden email].
> For more options, visit https://groups.google.com/d/optout.

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When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


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