Re: [base] GenePix Alternitives?

Wed, 02 Aug 2006 02:32:21 -0700

Hi Everybody!!

I have a problem (again!) with a .gpr file. I have configure  a RAW data importer to parser GenePix .gpr file. The plugin configuration is:

Block \Block\
Column \Column\
Data footer
Data header Block\tColumn
Data splitter \t
Header ATF\t1.0
Ignore
Max data columns
MetaGridX
MetaGridY
Min data columns
CV
Background pixels
Channel 1 background mean
Channel 1 background median
Channel 1 background standard deviation
Channel 1 foreground mean
Channel 1 foreground median
Channel 1 foreground standard deviation
Percent saturated pixels
Percent pixels within 1 standard deviation
Percent pixels within 2 standard deviations
Channel 2 background mean
Channel 2 background median
Channel 2 background standard deviation
Channel 2 foreground mean
Channel 2 foreground median
Channel 2 foreground standard deviation
Percent saturated pixels
Percent pixels within 1 standard deviation
Percent pixels within 2 standard deviations
Spot diameter
Foreground pixels
Flags
M value
Standard deviation of ratios
Rgn R2
Rgn ratio
Raw data type genepix
Reporter ID \ID\
Row
Remove quotes true
X
Y

I minimize the file to some columns (Block, Column, ID) to try to debug the plugin. Base2 give me the next error advise:

Error: File 'File[id=31; name=prueba9.gpr]' cannot be imported by this plugin.
InvalidDataException: File 'File[id=31; name=prueba9.gpr]' cannot be imported by this plugin.

The .gpr file that im using is:

ATF    1.0
31    1
Type=GenePix Results 3   
DateTime=2005/02/26 13:51:20   
Settings=1.26.10.gps   
GalFile=Impresion3gal27enero04.gal   
PixelSize=10   
"Wavelengths=635    532"   
"ImageFiles=1.26.10_750_760 24h-4.tif 2    1.26.10_750_760 24h-4.tif 3"   
NormalizationMethod=None   
"NormalizationFactors=1    1"   
JpegImage=1.26.10.jpg   
StdDev=Type 1   
RatioFormulations=W1/W2 (635/532)   
Barcode=   
BackgroundSubtraction=LocalFeature   
ImageOrigin=1640, 4240
JpegOrigin=1640, 4240
Creator=GenePix Pro 4.1.1.4
Scanner=GenePix 4000B [92593]
FocusPosition=5
Temperature=27.79
LinesAveraged=2
Comment=
"PMTGain=750    760"
"ScanPower=100    100"
"LaserPower=3.54    1.82"
"LaserOnTime=6532    6557"
"Filters=    "
ScanRegion=164,424,2000,5952
Supplier=BioRobotics
ArrayerSoftwareName=TAS Application Suite (MicroGrid II)
ArrayerSoftwareVersion=2.4.0.2       
Block    Column    ID
1    1    cal2
1    2    cal2

Could someone help me? Could someone send me a test .gpr file or a valid configuration plugin?

Thanks a lot

------------------------------------------------------------------------------------------------------------------------------
Pablo Lemos Ochandio - Analista de Sistemas Fisicos
Instituto Valenciano de Investigaciones Agrarias (IVIA)
Crta Moncada - Naquera Km 4.5
46113 - Moncada
Valencia
Spain 
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