[BioC] read.GenePix problem.

[Jean Yee Hwa Yang]

Hi Ivan,

You did read the data into test. When you type
> test
it will provide some basic summary information about the marrayRaw object.

You can tell that data was read in by checking part C of the output.

> 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

To extact the actual log-ratios type
maM(test)

Cheers

Jean

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Jean Yee Hwa Yang			 jean at biostat.ucsf.edu
 Division of Biostatistics,		   Tel: (415) 476-3368
 University of California,		   Fax: (415) 476-6014
 500 Parnassus Avenue, MU 420-W,  San Francisco, CA 94143-0560
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Fri, 6 Jun 2003, Ivan Borozan wrote:

> 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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