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From: Todd P. <tf...@nc...> - 2001-08-14 20:20:24
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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 |