[BioC] read.GenePix problem.

[Ivan Borozan]

Jean hi,

thanks, the  maM(test) works fine however if i do:

maRawPlots(test)

i get:
Error in rep(NA, maNspots(L)) : invalid number of copies in "rep". 

any help ?

all the best,
Ivan.

On Fri, 6 Jun 2003, Jean Yee Hwa Yang wrote:

> 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
> >  
> > 
> > --
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
> 

--