Hi Guido.
On Mon, Apr 11, 2011 at 1:42 PM, Hooiveld, Guido <guido.hooiv...@wur.nl> wrote:
> Hi Henrik,
>
> Thanks for your continuous efforts on aroma.affymetrix!
>
> With interest I have read the change-log, but do you mind spending a few
> words what exactly is meant with this argument, and why this is implemented?
> o Added argument 'uniquePlm' to doRMA() and doGCRMA() for doing
> probe-level summarization on unique probe sets only.
>
> I looked up the source code to see what exactly will happen when this
> argument is passed, but i wasn't able to fully understand it. I guess it is
> related to this thread at the BioC mailing list?
> http://article.gmane.org/gmane.science.biology.informatics.conductor/33688
Yes, it certainly looks related, but they are actual "opposite"
approaches. In the above email thread you can read that:
"in just.rma and rma, it was assumed that each probe could be in at
most 1 probeset. once a probe was used, it cannot be reused. on the ST
arrays, some probes can be in many probesets... so if you use rma,
eventually, all the probes in a probeset have been used once by the
time the current probeset needs it & you get NA's."
whereas in help("createUniqueCdf.AffymetrixCdfFile",
package="aroma.affymetrix") you can read that:
"In some cases, single probes map to multiple genome locations. In
cases where you may later want to store a probe estimate (e.g. a probe
effect or a residual), you will not be able to store more than one per
cell. The unique CDF facilitates this by making the cell indices
unique (essentially copying the multimapping probes)."
When you use unique=TRUE in doRMA() or doGCRMA() it will first create
a new set of CEL files using the unique CDF as a template. For
instance, say that two different probesets in the original CDF
contains cells indexed as (1,2,3) and (4,5,2), which means that they
share probe #2. In the "unique" CDF, these will be indexed as (1,2,3)
and (4,5,6) making it appear that the two probesets have unique sets
of probes. Now, since the CEL files map to the original CDF, in
order to be able to use the "unique" CDF, a new set of "uniquified"
CEL files that map to the "unique" CDF have to be created. That is
created by csU <- convertToUnique(cs), which BTW also creates the
"unique" CDF, if missing.
The "trick" of using a "unique" CDF mapping originates mainly from
Mark Robinson and is used in:
Vignette: MAT - Tiling array analysis (Promoter 1.0R)
http://aroma-project.org/vignettes/MAT-TilingArrayAnalysis
as well as in:
Mark Robinson's FIRMAGene method (see his sup3.R aroma.affymetrix script)
http://bioinf.wehi.edu.au/folders/firmagene/
http://aroma-project.org/addons/
Hope this clarifies things a bit.
/Henrik
PS. BTW, the 'Author' section of
help("createUniqueCdf.AffymetrixCdfFile" is wrong - all credits to
Mark Robinson.
>
> Thanks & regards,
> Guido
>
>
> ---------------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> email: guido.hooiv...@wur.nl
> internet: http://nutrigene.4t.com
> http://www.researcherid.com/rid/F-4912-2010
>
>
> -----Original Message-----
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
> Sent: Monday, April 11, 2011 21:39
> To: aroma-affymetrix
> Subject: [aroma.affymetrix] aroma.affymetrix v2.1.0 released
>
> Hi,
>
> aroma.affymetrix v2.1.0 and friends have been released. Grab the new version
> by:
>
> source("http://aroma-project.org/hbLite.R";);
> hbInstall("aroma.affymetrix");
>
>
>
> --
> 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 aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
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 aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
