Download Agilent CytoGenomics 3.0

Table 3
List of parameters and options contained within the FULL text output file (FEPARAMS table)
Protocol Step
Parameters
Type/Options
Description
Place Grid
GridPlacement_enableUseCentralPack
integer
1 = True
0 = False
Indicates status of the Use central part of
pack for slope and skew calculation flag
Place Grid
GridPlacement_placementMode
integer
Mode of grid placement
0
1
Allow the grid to distort
Place the grid rigidly allowing only
translation and rotation
Optimize Grid Fit
IterativeSpotFind_CornerAdjust
integer
0 = False
1 = True
Indicates whether or not the grid will be
adjusted for better fit by looking at corner
spots on the microarray
Optimize Grid Fit
IterativeSpotFind_AdjustThreshold
float
Grid will be adjusted if absolute average
difference between grid and spot positions
is greater than this fraction
Optimize Grid Fit
IterativeSpotFind_MaxIterations
integer
Maximum number of times spot finder
algorithm is run to optimize the grid fit
Optimize Grid Fit
IterativeSpotFind_FoundSpot
Threshold
float
Grid will be adjusted if this fraction or more
of the features are considered found by the
spot finder algorithm
Optimize Grid Fit
IterativeSpotFind_NumCornerFeatures
integer
Indicates the square area of features in
each corner of the microarray to be used to
calculate the average difference
Find Spots
SpotAnalysis_Version
text
Version of the spot analysis algorithm
Find Spots
SpotAnalysis_weakthresh
float
Minimum difference between the average
intensities of feature and background after
Kmeans Initialization
Find Spots
SpotAnalysis_MinimumNumPixels
integer
Minimum number of pixels required for the
spot analysis
Find Spots
SpotAnalysis_RegionOfInterest
Multiplier
float
Multiplier that defines how big the Region
of Interest (ROI) is in terms of nominal spot
spacing
Find Spots
SpotAnalysis_convergence_factor
float
Convergence factor of KMeans algorithm
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Feature Extraction for CytoGenomics Reference Guide