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@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 R????" "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@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > --