[BioC] read.GenePix problem.

[Ivan Borozan]

hi all,

if i try to create the obect class marrayRaw with the read.GenePix() 
function i get :

1) using test<-read.GenePix("test.gpr",sep="\t")

[1] 29
[1] "Reading ./M106a.gpr"
Pre-normalization intensity data:        Object of class marrayRaw. 

Number of arrays:       1 arrays.
 
A) Layout of spots on the array: 
Array layout:    Object of class marrayLayout. 

Total number of spots:
Dimensions of grid matrix:               rows by  cols
Dimensions of spot matrices:             rows by  cols

Currently working with a subset of  spots.

Control spots: 

Notes on layout: 


B) Samples hybridized to the array: 
Object of class marrayInfo. 


Number of labels:  0  
Dimensions of maInfo matrix:   rows by   columns

Notes: 


C) Summary statistics for log-ratio distribution: 
           Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
M106a.gpr -4.52    0.23   0.71 0.94    1.38 8.72 2063

D) Notes on intensity data: 
GenePix Data

which is obviously no good.

what am i doing wrong ?



all the best,

ivan.

the header of my gpr file is the following

ATF	1.0
24	43    
"Type=GenePix Results 1.2"
"DateTime=2002/10/03 11:37:59"
"Settings=L:\Program Files\GenePixPro3\iji.gps"
"GalFile=E:\Axon\Params\H19K3\H19k3b.gal"
"Scanner=GenePix 4000A"
"Comment="
"PixelSize=10"
"ImageName=635 nm	532 nm"
"FileName=I:\LH66-73\LH68-71\LH68-2-Cy5-670-Cy3-650.tif	
I:\LH66-73\LH68-71\LH68-2-Cy5-670-Cy3-650.tif"
"PMTVolts=670	650"
"NormalizationFactor:RatioOfMedians=1.0787"
"NormalizationFactor:RatioOfMeans=1.07502"
"NormalizationFactor:MedianOfRatios=1.07435"
"NormalizationFactor:MeanOfRatios=0.751559"
"NormalizationFactor:RegressionRatio=1.48559"
"JpegImage=L:\ Data\Limin\Liver project\LH (Biopsy)Exp\LH66-73\raw 
data\LH68-2-Cy5-670-Cy3-650.jpg"
"RatioFormulation=W1/W2 (635 nm/532 nm)"
"Barcode="
"ImageOrigin=840, 14460"
"JpegOrigin=2340, 16120"
"Creator=GenePix Pro 3.0.0.98"
"Temperature=1.45"
"LaserPower=2.51	2.6"
"LaserOnTime=52807	53773"
"Block"	"Column"	"Row"	"Name"	"ID"	"X"	"Y"	"Dia."	
"F635 Median"	"F635 Mean"	"F635 SD"	"B635 Median"	"B635 
Mean"	"B635 SD"	"% > B635+1SD"	"% > B635+2SD"	"F635 % Sat."	
"F532 Median"	"F532 Mean"	"F532 SD"	"B532 Median"	"B532 
Mean"	"B532 SD"	"% > B532+1SD"	"% > B532+2SD"	"F532 % Sat."	
"Ratio of Medians"	"Ratio of Means"	"Median of Ratios"	
"Mean of Ratios"	"Ratios SD"	"Rgn Ratio"	"Rgn R²"	"F 
Pixels"	"B Pixels"	"Sum of Medians"	"Sum of Means"	"Log 
Ratio"	"F635 Median - B635"	"F532 Median - B532"	"F635 Mean - B635"	
"F532 Mean - B532"	"Flags"
1	1	1	H78273	239536	2450	16370	100	55	56	
20	30	33	10	73	57	0	93	93	33	
47	49	16	81	58	0	0.543	0.565	0.506	
1.154	2.038	0.233	0.162	80	472	71	72	-0.880	25	
46	26	46	0
 

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