[GeneX-dev] Re: GeneX Problems

[Todd P. <tf...@nc...>]

This didn't make the sourceforge list originally (due to message size) so
I'm fwd'g again without the huge attachments. I also meant to say '2 decimal
points'; i.e., 1..94E+05 instead of '2 decimal places' in item 2.

Todd

----- Original Message -----
From: "Todd Peterson" <tf...@nc...>
To: "Rick Tarleton" <tar...@cb...>; <ge...@nc...>
Cc: <gen...@li...>
Sent: Tuesday, August 14, 2001 10:54 AM
Subject: Re: Genex problems


> OK...here's what I figured out:
>
> 1. The sequence feature col file did not have a valid extra-type
specified.
> 2. The spot measurement file has several floating point values with 2
> decimal places in them.
> 3. Line 255 of the layout file has 2 extra columns at the end of the line.
> 4. Managed to create an array layout with 4942 user sequence features and
> 4942 array layout spots when I did the first array measurement, it got an
> error message of many missing values. It did create the measurement,
though,
> with 4242 spots found. Did verify that the first one it complained about
was
> not there (id=4033). Have included the Curation Tool output after
minimally
> marking up 2 data columns.
>
> Todd Peterson
> Software Developer
> NCGR
>
> ----- Original Message -----
> From: "Rick Tarleton" <tar...@cb...>
> To: <ge...@nc...>
> Sent: Saturday, August 11, 2001 6:24 AM
> Subject: Genex problems
>
>
> > Hi:
> >
> > I have been hammering away at the curation tool on Genex for most of
> > this week and can't get it quite figured out - hope you can help.
> >
> > We have custom glass arrays (mguide arrayer) read on a GMS scanner and
> > the data processed through microarray suite to obtain ratios.  Genex
> > seems to be set up nicely on a Linux machine and I am trying to use the
> > curation tool on a windows machine (not a real x-windows fan).
> >
> > I think my biggest problem is in making the column definition files - I
> > thought I had it figured out but apparently not.  I am mostly going from
> > the test data supplied to figure this out - the tutorial does not help a
> > lot there - is there a better help file on how to do this?
> >
> > Anyway, I seem to be able to get the sequence feature, layout and spot
> > measurement data read in OK (it gets validated) but then I get into
> > problems.  First, in the 'Hybridization and Detection' page, when I
> > select 'edit/view' for the 'array layout' line, I get the 'table
> > name:array layouts' window which lists the two test data - 'pat brown's
> > and the panorama'.  When I try to 'add row' to this list, nothing
> > happens - likewise if I try to 'use row as template'.  I can edit one of
> > the existing layouts (mod/view) - which I have done, and proceeded.
> > This opens the 'edit array layout information' window.  This window
> > shows that I have the expected number of  'view user sequence features'
> > - in this case 4992 - but the 'view array layout spots' is '0'.  If  I
> > proceed on from this, to the 'edit array measurement' window and then
> > try to save the setup, I get a meassage for each of the entries that
> > "the selected array does not have an array layout spot for the array
> > layout spot ......"
> >
> > So that is where I am stuck.
> >
> > I am attaching the data files and the column definition files.  The seq
> > feature and layout entries are from the 0807.gip file and use the
> > arrayDb and layout_gip col def  files, respectively.  The spot intensity
> > file is SI 0807... and uses the 'spot_meas' col def file.
> >
> > I would appreciate any help or suggestions - particularly any additional
> > help files on inputting these data.  I like the look of the package so
> > far.  We have been working on adapting the ArrayDB program from the
> > NCHGR for our use so I realize the difficulties involved.
> >
> > Thanks in advance
> >
> > Rick

Todd Peterson
NCGR
mailto:tf...@nc...
(505) 995-4417