Hello All,
We're attempting to use base2 to manage antibody ELISA microarray data. We
print antibodies on slides divided into 16 wells, with one array block printed
per well, and with all wells printed with the same antibodies in the same
pattern.
My Problem: I've been trying use the printmap importer plugin to import a TAM
file into an Assay Design. The plugin runs without an error, but only the
blocks from the TAM file are inserted, whereas the features are not, as per
this message: " Done: 0 feature(s) inserted; 16 block(s) inserted" (the full
job report is shown below).
Does anyone have ideas on how to solve this problem? My guess is that my the
plate file that is associated with the Assay Design (via "Manage Plates") is
not being read corrrectly, if at all.
I've checked my TAM file, and it appears to be correctly formatted (excerpt
below).
I have suspected that the plate name values in the TAM file records are not
identifying the correct plate within base. I have it set to match the
"Position" value that corresponds to the correct plate on the Array Designs
page.
I'm running base-2.2.1 on Red Hat Enterprise Linux 4.
Any enlightenment on my situation would be greatly appreciated.
Thanks,
Jim Collett
James R. Collett, Ph.D.
Postdoctoral Scientist
Battelle Memorial Institute
Biological Sciences Division
Pacific Northwest National Laboratory
PO Box 999
MS P7-58
Richland, WA 99354
voice: (509) 376-2954
fax: (509) 372-6544
-------------------------
View job -- Run plugin: Print map importer
javascript:Main.openTabControlHelp('2dc508b2c1deb15a', 'main', 'null')
Name Run plugin: Print map importer
Description
Priority 4 (1 = highest, 10 = lowest)
Status Done: 0 feature(s) inserted; 16 block(s) inserted
Percent complete
100%
Created 2007-02-13 20:58:45
Started 2007-02-13 20:59:30
Ended 2007-02-13 20:59:30
Server lims
Plugin Print map importer
Configuration - none -
-----------------------------------------------
Excerpt from my TAM file:
[Block15]
MetaGridX=,1
MetaGridY=,8
OriginX=,3250
OriginY=,66300
BlockSizeX=,12
BlockSizeY=,10
SpacingX=,500
SpacingY=,500
[Block16]
MetaGridX=,2
MetaGridY=,8
OriginX=,15250
OriginY=,66300
BlockSizeX=,12
BlockSizeY=,10
SpacingX=,500
SpacingY=,500
[mapping]
1,1,1,1,,1,1,1,Cy3,Cy3_IgG_NoLot1,1
1,1,1,2,,1,1,1,Cy3,Cy3_IgG_NoLot1,1
1,1,1,3,,1,1,1,Cy3,Cy3_IgG_NoLot1,1
1,1,1,4,,1,3,2,EMPTY,EMPTY,1
1,1,1,5,,1,3,2,EMPTY,EMPTY,1
1,1,1,6,,1,3,2,EMPTY,EMPTY,1
1,1,1,7,,1,3,2,EMPTY,EMPTY,1
1,1,1,8,,1,3,2,EMPTY,EMPTY,1
1,1,1,9,,1,3,2,EMPTY,EMPTY,1
1,1,1,10,,1,3,2,EMPTY,EMPTY,1
1,1,1,11,,1,3,2,EMPTY,EMPTY,1
1,1,1,12,,1,1,1,Cy3,Cy3_IgG_NoLot1,1
1,1,2,1,,1,3,1,AmR,Amr_BAN025061,1
1,1,2,2,,1,3,1,AmR,Amr_BAN025061,1
1,1,2,3,,1,3,1,AmR,Amr_BAN025061,1
1,1,2,4,,1,3,1,AmR,Amr_BAN025061,1
1,1,2,5,,1,2,11,CD14,CD14_AW104611,1
1,1,2,6,,1,2,11,CD14,CD14_AW104611,1
1,1,2,7,,1,2,11,CD14,CD14_AW104611,1
1,1,2,8,,1,2,11,CD14,CD14_AW104611,1
1,1,2,9,,1,2,10,EGF,EGF_cAb_KitNoLot1,1
1,1,2,10,,1,2,10,EGF,EGF_cAb_KitNoLot1,1
1,1,2,11,,1,2,10,EGF,EGF_cAb_KitNoLot1,1
1,1,2,12,,1,2,10,EGF,EGF_cAb_KitNoLot1,1
1,1,3,1,,1,2,8,Esel,Esel_DEN024031,1
1,1,3,2,,1,2,8,Esel,Esel_DEN024031,1
1,1,3,3,,1,2,8,Esel,Esel_DEN024031,1
1,1,3,4,,1,2,8,Esel,Esel_DEN024031,1
1,1,3,5,,1,2,9,EGFR,EGFR_AUC036051,1
1,1,3,6,,1,2,9,EGFR,EGFR_AUC036051,1
1,1,3,7,,1,2,9,EGFR,EGFR_AUC036051,1
1,1,3,8,,1,2,9,EGFR,EGFR_AUC036051,1
----------------------------------------------------------
Contents of my plate file in position 1:
Plate Row Column ReporterID
1 1 1 Cy3_IgG_NoLot1
1 1 2 VEGF_ZUO55071
1 1 3 uPAR_CEP01_1
1 1 4 TNFa_AVR11_1
1 1 5 TGFa_ANR015041
1 1 6 RANTES_JA075011
1 1 7 PSA_ITH02
1 1 8 MMP9_DJ0015061
1 1 9 MMP2_DWB034081
1 1 10 MMP1_DWK015041
1 1 11 PDGF_AA_DXC075051
1 1 12 IL18_CL_125-2H_1
1 2 1 IL1a_GX145111
1 2 2 IGF1_BIM03308
1 2 3 ICAM1_BC0013071
1 2 4 HGF_AWW03
1 2 5 HER2_cAb_NoLot1
1 2 6 HB_EGF_PX045051
1 2 7 bFGF_HR046011
1 2 8 Esel_DEN024031
1 2 9 EGFR_AUC036051
1 2 10 EGF_cAb_KitNoLot1
1 2 11 CD14_AW104611
1 2 12 CA15_3_M8071022_275
1 3 1 AmR_BAN025061
1 3 2 EMPTY
-------------------------------------------------------------------------
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