Re: [Gusdev-rad-issues] GenePixElementResult

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

Hi Josef,
if these are important to you they can be added to the view (you might=20
want to file a bug on the tracker so we can keep it in mind for future=20
releases). I see that the ArrayVision view of ElementResultImp, for=20
example, has these.
Note that there are other measures in the typical GenePix output file that=
=20
have not been put into the view intentionally, as they can be derived from=
=20
those already in, but I don't think this is the case for X and Y.
A note: I think that X and Y might be assay-dependent, in which case they=
=20
do indeed belong to a view of RAD.ElementResultImp. If however they were=20
the same for all assays on the same array they they should be placed in=20
the RAD.Spot view of ElementImp (e.g. the ShortOligo view has these for=20
Affy). I think though that it's the former case, can you confirm?
Elisabetta

  ---

On Tue, 22 Nov 2005, Josef Jurek wrote:

>
>
> In looking over the several typical output files of GenePix,
> I see that most of the important values of these files map
> to fields of the RAD.GenePixElementResult view:
>
>     GenePix                  RAD table
>
>     X                      ?
>     Y                      ?
>     Dia.                   RAD.GenePixElementResult.SPOT_DIAMETER
>     F635 Median            RAD.GenePixElementResult.FOREGROUND_MEDIAN
>     F635 Mean              RAD.GenePixElementResult.FOREGROUND_MEAN
>     F635 SD                RAD.GenePixElementResult.FOREGROUND_SD
>     B635 Median            RAD.GenePixElementResult.BACKGROUND_MEDIAN
>     B635 Mean              RAD.GenePixElementResult.BACKGROUND_MEAN
>     B635 SD                RAD.GenePixElementResult.BACKGROUND_SD
>     % > B635+1SD           RAD.GenePixElementResult.PERCENT_OVER_BG_PLUS_=
ONE_SD
>     % > B635+2SD           RAD.GenePixElementResult.PERCENT_OVER_BG_PLUS_=
TWO_SDS
>     F635 % Sat.            RAD.GenePixElementResult.PERCENT_FOREGROUND_SA=
TURATED
>     ...                    ...
>     F Pixels               RAD.GenePixElementResult.NUM_FOREGROUND_PIXELS
>     B Pixels               RAD.GenePixElementResult.NUM_BACKGROUND_PIXELS
>     Circularity            RAD.GenePixElementResult.CIRCULARITY
>
>
> however as far as I can tell, there is no place in the view to put
> the values of the columns that are labeled "X" and "Y" from a GenePix
> output file.  GenePix describes these values as follows
>
>    X     the X-coordinate in =C2=B5m of the center of the feature-indicat=
or associated with
>          the feature, where (0,0) is the top left of the image.
>
>    Y     the Y-coordinate in =C2=B5m of the center of the feature-indicat=
or associated with
>          the feature, where (0,0) is the top left of the image.
>
> This is important information that we do not want to toss away.
> Is this an oversight, or have I missed something?
>
> I hope columns for these two values can be added to this table/view.
> We will have to go a head an this columns in our locally installed
> version of RAD anyways, as we need this.
>
> Thanks Josef
>
>
>
>
> Josef Jurek
>
> Daphne Preuss Laboratory
> Molecular Genetics and Cell Biology
> The University of Chicago
> ju...@cs...
>
> voice: (773) 834-3985
> fax:   (773) 702-6648
>
>
>
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