Question: mean vs median of pixel values within spot mask wasRe: something weird with read.maimages and .gpr files
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gravatar for Pita
14.7 years ago by
Pita120
Pita120 wrote:
It seems that I answered my own question .... There was a typo that was entered into the Genepix software so the output would not parse. Limmas read.maimages looks specifically for the F532 Mean for the R channel, instead F594 Mean was written Since it is the case that the Mean of the pixels in the pot mask are used in limma as default: are they any arguments for using the mean values over the median values? Would the assumption here be that the spot morphology must be impeccable? Peter At 03:48 PM 2/25/2005, Pita wrote: >what can trigger the following error? I have imported many genepix >files without any problem > > >> RG.new.gpr <- read.maimages(files.new,"genepix",wt.fun=wtflags(0.1)) > >Error in "[.data.frame"(obj, , columns$Gf) : > > undefined columns selected > >This is with limma version 1.8.22 > > >Peter > >P.S. Here is a snippet of the first .gpr file: > >ATF 1.0 >29 56 >"Type=GenePix Results 3" >"DateTime=2005/01/26 14:13:02" >"Settings=" >"GalFile=C:\Axon\Params\ImmunArray2.gal" >"PixelSize=10" >"Wavelengths=635 594" >"ImageFiles=Y:\one\two\IMMUNOARRAY\26.01.05\13012006_SEKA0137-01_Cy5_ 26.01.05.tif.tif >0 Y:\one\two\IMMUNOARRAY\26.01.05\13012006_HURR_Cy3_26.01.05.tif 0" >"NormalizationMethod=None" >"NormalizationFactors=1 1" >"JpegImage=C:\Axon\Data\13012006_SEKA0137-01_Cy5_0026.jpg" >"StdDev=Type 1" >"RatioFormulations=W1/W2 (635/594)" >"FeatureType=Circular" >"Barcode=" >"BackgroundSubtraction=LocalFeature" >"ImageOrigin=0, 0" >"JpegOrigin=1190, 940" >"Creator=GenePix Pro 6.0.0.76" >"Scanner=4000 680056" >"FocusPosition=0" >"Temperature=0" >"LinesAveraged=1" >"Comment=" >"PMTGain=0 0" >"ScanPower=100 100" >"LaserPower=0 0" >"Filters= " >"ScanRegion=0,0,2022,3665" >"Supplier=" >"Block" >"Column" "Row" "Name" "ID" "X" "Y" "Dia." "F635 >Median" "F635 Mean" "F635 SD" "F635 CV" "B635" "B635 >Median" "B635 Mean" "B635 SD" "B635 CV" "% > >B635+1SD" "% > B635+2SD" "F635 % Sat." "F594 Median" "F594 >Mean" "F594 SD" "F594 CV" "B594" "B594 Median" "B594 >Mean" "B594 SD" "B594 CV" "% > B594+1SD" "% > >B594+2SD" "F594 % Sat." "Ratio of Medians (635/594)" "Ratio of Means >(635/594)" "Median of Ratios (635/594)" "Mean of Ratios (635/594)" >"Ratios SD (635/594)" "Rgn Ratio (635/594)" "Rgn R2 >(635/594)" "F Pixels" "B Pixels" "Circularity" "Sum of Medians >(635/594)" "Sum of Means (635/594)" "Log Ratio >(635/594)" "F635 Median - B635" "F594 Median - B594" "F635 Mean - >B635" "F594 Mean - B594" "F635 Total Intensity" "F594 Total >Intensity" "SNR 635" "SNR 594" "Flags" "Normalize" "Autoflag" >1 1 1 "DUSP2:Hs.1183:AA759046" "1321598" >1540 1160 100 2528 2522 1254 49 0 >0 90 154 171 100 97 0 1971 1990 1077 > 54 0 0 59 123 208 100 97 0 > 1.283 1.267 >1.363 1.339 2.275 1.272 0.575 80 546 100 4499 >4512 0.359 2528 1971 2522 >1990 201729 159237 15.792 15.699 0 0 0 >1 2 1 "DUSP2:Hs.1183:AA759046" "1321598" >1750 1170 120 2686 2625 1525 58 0 >0 84 174 207 97 95 0 1841 2014 1266 > 62 0 0 47 106 225 96 95 0 > 1.459 1.303 >1.352 1.417 2.660 1.326 0.630 120 693 100 4527 >4639 0.545 2686 1841 2625 >2014 314976 241629 14.603 18.557 0 0 0 >1 3 1 "MYL4:Hs.356717:AA705225" "461425" >1940 1160 110 7604 7657 2219 28 0 >0 77 142 184 100 100 0 4055 4284 1390 > 32 0 0 65 133 204 100 100 0 > 1.875 >1.787 1.684 1.811 1.524 2.029 0.741 80 572 100 >11659 11941 0.907 7604 4055 >7657 4284 612532 342716 53.380 31.722 0 0 0 >1 4 1 "MYL4:Hs.356717:AA705225" "461425" >2140 1160 110 6585 7117 2955 41 0 >0 84 167 198 100 100 0 3261 3319 1518 > 45 0 0 73 164 224 96 95 0 > 2.019 2.144 >2.060 2.423 2.458 2.355 0.736 80 620 100 9846 >10436 1.014 6585 3261 7117 >3319 569339 265548 42.114 19.793 0 0 0 >1 5 1 "PSMB8:Hs.180062:AA181300" "624360" >2350 1160 110 2433 2535 1160 45 0 >0 79 146 184 100 98 0 2484 2641 1292 > 48 0 0 83 219 263 97 97 0 > 0.979 0.960 >0.951 0.989 2.062 0.908 0.637 80 579 100 4917 >5176 -0.030 2433 2484 2535 >2641 202824 211288 16.822 11.680 0 0 0 >1 6 1 "PSMB8:Hs.180062:AA181300" "624360" >2540 1170 120 2155 2327 1336 57 0 >0 72 139 193 97 95 0 2260 2256 1207 > 53 0 0 53 129 243 95 92 0 > 0.954 1.031 >0.961 0.998 2.537 1.101 0.660 120 692 100 4415 >4583 -0.069 2155 2260 2327 >2256 279193 270688 16.223 17.078 0 0 0 >1 7 1 "RAD51C:Hs.412587:R37145" "26997" >2750 1160 90 1743 1788 796 44 0 0 >76 143 188 100 98 0 2250 2460 1181 48 > 0 0 66 161 243 100 98 0 0.775 > 0.727 >0.719 0.730 2.097 0.617 0.472 52 420 100 3993 >4248 -0.368 1743 2250 1788 >2460 92995 127944 11.972 14.870 0 0 0 >1 8 1 "RAD51C:Hs.412587:R37145" "26997" >2950 1160 100 1184 1237 725 58 0 0 >74 134 181 100 95 0 1938 1806 998 55 > 0 0 66 147 222 95 92 0 0.611 > 0.685 >0.579 0.692 2.521 0.599 0.484 80 540 100 3122 >3043 -0.711 1184 1938 1237 >1806 98992 144478 8.679 11.837 0 0 0 >1 9 1 "SHC1:Hs.433795:R52961" "40303" >3140 1160 90 2265 2434 1153 47 0 0 83 >160 192 100 100 0 2064 2021 1040 51 0 > 0 73 140 191 98 96 0 1.097 1.204 >1.232 1.289 2.207 1.187 0.553 52 414 100 4329 >4455 0.134 2265 2064 2434 >2021 126582 105071 14.694 13.914 0 0 0 >1 10 1 "SHC1:Hs.433795:R52961" "40303" >3350 1170 100 2040 2032 1088 53 0 0 >75 122 162 100 100 0 1771 1847 1021 55 > 0 0 61 119 195 98 96 0 1.152 > 1.100 >1.104 1.141 2.092 1.121 0.569 80 532 100 3811 >3879 0.204 2040 1771 2032 >1847 162549 147753 16.041 15.008 0 0 0 >1 11 1 "TYROBP:Hs.9963:H12338" >"148469" 3550 1170 110 15761 14143 5861 41 >21 21 106 172 162 100 100 0 744 884 > 592 66 0 0 42 101 240 91 86 >0 21.156 >15.975 17.541 19.010 2.619 18.419 0.594 80 590 100 >16484 15006 4.403 15740 744 14122 884 1131446 >70752 81.610 8.337 0 0 0 >1 12 1 "TYROBP:Hs.9963:H12338" >"148469" 3750 1170 110 15557 14415 6677 46 0 >0 103 178 172 100 100 0 865 916 602 > 65 0 0 47 131 278 90 80 0 > 17.985 15.737 >16.305 18.014 2.349 18.037 0.619 80 590 100 16422 >15331 4.169 15557 865 14415 916 1153181 >73243 80.404 6.634 0 0 0 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >
limma trigger • 569 views
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