[base] reporter lists

[Bob MacCallum]

Hi,

Probably a dumb question, but I don't understand reporter lists in BASE2.

I see that I can create them from the View-Reporter lists menu.  That seems
simple enough, although I haven't tried it.

But a more likely scenario is that I'd want to create them from a filtered
bioassayset (or is my thinking corrupted by BASE1?).  I don't see any kind of
export option in the experiment explorer (e.g. from Reporter search), although
in BASE1 this was very clunky.  I would basically like to export the reporters
from a bioassayset (or create a reporter list) and then paste/upload them into
BioMart.  I could export a MEV or BASEfile but this would be overkill.

Also, can reporter lists be used in filter expressions in BASE2?

many thanks,
Bob

-- 
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]

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Re: [base] base-2.3.2 and exporting basefiles - the last line of the bioassay set is absent

[Bob MacCallum]

I have just found a small bug (and fix) related to this topic and added a new
ticket:

http://base.thep.lu.se/ticket/938


Johan Enell writes:
  I have added this as a ticket (http://base.thep.lu.se/ticket/671) and I 
  will take a closer look at it.
  
  /Johan
  
  
  Chad Matsalla wrote:
   Greetings!
  
   I've discovered a problem with exporting BASEfiles. I discovered this while
   trying to run the BASE1PluginExecuter and unsurprisingly found the same
   problem when trying to export data from a BioassaySet. The problem is that
   the last row of data is absent from the export.
  
   Here's what I observered:
  
   1. The Raw Bioassay has 31200 rows. When I go to the 'Raw Bioassay' page,
   'Raw Data' page  and 'Export' it I get all of the rows as a tab-delimited
   text file. Yay!
  
   2. I go Experiments-Chad's Experiment-Bioassay Sets and click 'Export
   Data', select BASEfile and these parameters:
   Average on reporters: false
   Export as matrix or serial basefile: Serial Basefile
   Fields: Int ch1, Int ch2, position
   Reporter: Reporter ID, Reporter Name
  
   The last row I see exported has the position 31199. Row 31200 is absent. A
   blank line is at the end of this file.
  
   3. Do everything the same as (2) but select 'Normal Basefile'.
  
   The last row I see exported has the position 31199. Row 31200 is absent. No
   blank line is at the end of this file.
  
  
   Thank you for your help,
  
   Chad Matsalla
   Plant Biotechnology Institute
   Saskatoon, Saskatchewan
  
  
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-- 
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]

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Re: [base] reporter lists

[Nicklas Nordborg]

Bob MacCallum wrote:
 
 Also, can reporter lists be used in filter expressions in BASE2?

Yes. They should show up in the expression builder. You need the 
internal ID of the reporter list so it's not very practical to enter 
those expressions by hand.

/Nicklas


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