Re: [GUSDEV] Affymetrix .CEL files

[Elisabetta M. <man...@pc...>]

Hi Dave,
let me clarify GUS vs Affy.
Affymetrix quantified results are of two types, corresponding to 2 
different level of analysis:

(i) probe-cell level results (e.g. from .CEL files), which contain 
intensity values for each individual probe cell on the chip; and
(ii) probe-set level results (e.g. obtained from MAS4 or MAS 5 and in the 
.CHP files, or from RMA or gcRMA) which contain *summarized* intensities 
for probe sets on the chip.

The GUS schema in principle supports storage of both:

(i) the probe cell results would go into a view of RAD.ElementResultImp 
(in fact there is a view to this end called RAD.AffymetrixCEL);
(ii) the probe set results would go to view of 
RAD.CompositeElementResultImp. For the latter, currently we  have views to 
accomodate MAS4 or 5 (RAD.AffymetrixMAS4 or RAD.AffymetrixMAS5) and 
RMA/gcRMA results (RAD.RMAExpress, which will actually be renamed RAD.RMA 
in the next GUS release).

Now, here at CBIL, we do not store or support loading of the .CEL file 
data in the database, because we really only use the probe-set level 
results in our applications, so we have no need to store .CEL in the db.
So the way we do it is as follows:
* for every Affymetrix assay, we have TWO related quantifications, one 
corresponding to the .CEL quantification and the other corresponding to 
whatever summarization quantification was created (e.g. with MAS4, MAS5, 
RMA);
* we place 2 entries in RAD.Quantifications, one pointing to the uri of 
the .CEL file (which we keep on our server) and one pointing to the uri 
of the probe-set level result file
* we however do not store the data from the .CEL file in RAD.AffymetrixCEL
* we only store the data from the probe-set level results 
in one of the RAD.CompositeElementResultImp views mentioned above.

The current plugin in GUS::Supported, as Junmin mentioned in the posting 
you are referring to, can be used to populate the data for the probe-set 
level results. As far as I know, we do not have currently a plugin to 
store the .CEL files in the db.
So the db allows for the latter, but you'd have to write your own plugin. 
We didn't find useful to store .CEL results in GUS, but again this depends 
on the type of applications you might be interested in.
Hope this helps,
Elisabetta


On Tue, 28 Aug 2007, Dave Hau wrote:

> I would like to import a number of Affymetrix .CEL files into the GUS
> database, which was installed from top of trunk from the GUS svn
> repository.  The CEL files each have some text headers, and then binary
> data afterwards.  So I suppose they are in CEL Version 4 format.
>
> Doing some search on previous posts, I came across this one:
>
> http://sourceforge.net/mailarchive/message.php?msg_id=Pine.LNX.4.61.0512141526200.18143%40hera.pcbi.upenn.edu
>
> It seems that at the time of the post (12/2005), the way these .CEL
> files would be imported was that the headers would go to one of the
> Affymetrix views (AffymetrixMAS4 or AffymetrixMAS5 or AffymetrixCEL),
> the actual file would sit in the file system, and we'd insert a row to
> the RAD.Quantification table with a URI pointing to the location of the
> .CEL file.
>
> Also, looking through the different plugins in both the Supported and
> Community folders, it seems LoadBatchArrayResults supports the cel4
> format.  Is this the plugin I should use?
>
> Any help would be much appreciated.  Thanks.
>
> Best regards,
> Dave Hau