Hi everyone I am working with my gpr files with bioconductor. I have a problem, which i believe could be trivial. I encounter a problem which sends an error message and i could not proceed after the read.maimages step. We use scanarrayexpress software (Perkin elmer) and stanford microarray chips to generate gpr files. I am giving you the output i got from R. Please let me know where ive gone wrong. > filenames <- c("hov163N.gpr", "hov169.gpr","hov171.gpr","hov172.gpr","hov175N.gpr","hov176.gpr","hov 206.gpr","hov207N.gpr","hov215.gpr","hov221N.gpr","hov222.gpr","hov226 .gpr","hov229.gpr","hov234.gpr","hov239.gpr") > data <- read.GenePix(filenames) Reading ... hov163N.gpr Reading ... hov169.gpr Reading ... hov171.gpr Reading ... hov172.gpr Reading ... hov175N.gpr Reading ... hov176.gpr Reading ... hov206.gpr Reading ... hov207N.gpr Reading ... hov215.gpr Reading ... hov221N.gpr Reading ... hov222.gpr Reading ... hov226.gpr Reading ... hov229.gpr Reading ... hov234.gpr Reading ... hov239.gpr > filenames [1] "hov163N.gpr" "hov169.gpr" "hov171.gpr" "hov172.gpr" "hov175N.gpr" [6] "hov176.gpr" "hov206.gpr" "hov207N.gpr" "hov215.gpr" "hov221N.gpr" [11] "hov222.gpr" "hov226.gpr" "hov229.gpr" "hov234.gpr" "hov239.gpr" > rg <- read.maimages(filenames, source="genepix") Read hov163N.gpr Read hov169.gpr Read hov171.gpr Read hov172.gpr Read hov175N.gpr Read hov176.gpr Read hov206.gpr Read hov207N.gpr Read hov215.gpr Read hov221N.gpr Read hov222.gpr Error in readGPRHeader(fullname) : File is not in Axon Text File (ATF) format Thank you for your time looking into this. Raja [[alternative HTML version deleted]]

Hi everyone, I forgot to attach the format of my gpr files. Here are the first few lines of my gpr files. ATF 1 21 82 Type=GenePix Results 2 DateTime=2008/05/31 12:02:37 Settings=Easy Quant GalFile=C:\Documents and Settings\Administrator\Desktop\stanford chip data\hov172.gal Scanner=Model: ProScanArray Serial No.:XXXXX Comment=<f1>Cyanine 3<f2>Cyanine 5<f1 offset="">0,0<f2 offset="">-1,0<comment> PixelSize=10 Wavelengths=543 nm 633 nm ImageFiles=C:\Documents and Settings\Administrator\Desktop\stanford chip data\Cyanine 3 42 30-5-08 [3].tif C:\Documents and Settings\Administrator\Desktop\stanford chip data\Cyanine 5 48 30-5-08 [4].tif PMTGain=42 48 NormalizationMethod=LOWESS NormalizationFactors=0.000 0.000 JpegImage= RatioFormulations=W2/W1(635/532) Barcode= ImageOrigin=1329 5869 JpegOrigin=0 0 Creator=ScanArray Express, Microarray Analysis System 4.0.0.4 Temperature=0.0 LaserPower=90 90 0 0 LaserOnTime=0 0 0 0 Block Column Row Name ID X Y Dia. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F3 Median F3 Mean F3 SD B3 Median B3 Mean B3 SD % > B3+1SD % > B3+2SD F3 % Sat. F4 Median F4 Mean F4 SD B4 Median B4 Mean B4 SD % > B4+1SD % > B4+2SD F4 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R² (635/532) Ratio of Medians (Ratio/2) Ratio of Means (Ratio/2) Median of Ratios (Ratio/2) Mean of Ratios (Ratio/2) Ratios SD (Ratio/2) Rgn Ratio (Ratio/2) Rgn R² (Ratio/2) Ratio of Medians (Ratio/3) Ratio of Means (Ratio/3) Median of Ratios (Ratio/3) Mean of Ratios (Ratio/3) Ratios SD (Ratio/3) Rgn Ratio (Ratio/3) Rgn R² (Ratio/3) F Pixels B Pixels Sum of Medians Sum of Means Log Ratio (635/532) Log Ratio (Ratio/2) Log Ratio (Ratio/3) F532 Median - B532 F635 Median - B635 F3 Median - B3 F4 Median - B4 F532 Mean - B532 F635 Mean - B635 F3 Mean - B3 F4 Mean - B4 Flags Normalize 1 1 1 Actin, beta ACTB 2424 7574 120 1751 1632 403 323 324 8 100 100 0 1743 1611 388 324 324 11 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.994 0.983 0.989 1.254 1.254 0.597 0.384 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88 86 2847 2596 -0.009 0 0 1428 1419 0 0 1309 1287 0 0 100 1 1 2 1 Actin, beta ACTB 2574 7569 110 1895 1807 306 324 327 9 100 100 0 1777 1684 316 322 326 12 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.926 0.918 0.927 1.024 1.024 0.372 0.129 0 0 0 0 0 0 0 0 0 0 0 0 0 0 78 75 3026 2845 -0.111 0 0 1571 1455 0 0 1483 1362 0 0 100 1 1 3 1 Ribosomal protein L13a RPL13A 2724 7564 120 5662 5125 1491 330 335 16 100 100 0 3592 3281 924 326 329 17 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.613 0.616 0.617 0.705 0.705 0.426 0.472 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88 86 8598 7750 -0.707 0 0 5332 3266 0 0 4795 2955 0 0 100 1 [[alternative HTML version deleted]]