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Sample GSM6301 Query DataSets for GSM6301
Status Public on Apr 15, 2004
Title AML 86
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 86
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680650LaserPower=3.894.66
Lot batch = shdj068
 
Submission date May 07, 2003
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL319
Series (1)
GSE425 Acute myeloid leukemia study

Data table header descriptions
ID_REF
CH1D_MEDIAN Median spot pixel intensity at Channel 1 with the median-background subtracted (CH1I_MEDIAN - CH1B_MEDIAN)
CH1I_MEDIAN Median spot pixel intensity at Channel 1
CH1_PER_SAT Percentage of spot pixels at Channel 1 that are saturated
CH1I_SD Standard deviation of the spot intensity at Channel 1
CH1B_MEAN Mean spot background in Channel 1
CH1B_MEDIAN Median spot background intensity in Channel 1
CH1B_SD Standard deviation of the spot background intensity in Channel 1
CH1D_MEAN Mean Channel 1 intensity with the median-background subtracted (CH1I_MEAN - CH1B_MEDIAN)
CH2I_MEAN Mean spot pixel intensity at Channel 2
CH2D_MEAN Mean spot pixel intensity at Channel 2 with the median-background subtracted (CH2I_MEAN - CH2B_MEDIAN)
CH2D_MEDIAN Median spot pixel intensity at Channel 2 with the median-background subtracted (CH2I_MEDIAN - CH2B_MEDIAN)
CH2I_MEDIAN Median spot pixel intensity at Channel 2
CH2_PER_SAT Percentage of spot pixels at Channel 2 that are saturated
CH2I_SD Standard deviation of the spot pixel intensity at at Channel 2
CH2B_MEAN Mean spot background intensity in Channel 2
CH2B_MEDIAN Median spot background intensity in Channel 2
CH2B_SD Standard deviation of the spot background intensity in Channel 2
CH2BN_MEDIAN Normalized value of median Channel 2 background (CH2B_MEDIAN/Normalization factor)
CH2DN_MEAN Normalized value of mean Channel 2 intensity with normalized background subtracted (CH2IN_MEAN - CH2BN)
CH2IN_MEAN Normalized value of mean Channel 2 intensity (CH2I_MEAN/Normalization factor)
CH2DN_MEDIAN Normalized value of median Channel 2 intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN)
CH2IN_MEDIAN Normalized value of median Channel 2 intensity (CH2_MEDIAN/Normalization factor)
CORR Coefficient of determination for the current regression value
DIAMETER Diameter in �m of the spot indicator
FLAG Type of flag associated with a spot (default=0)
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the medians of Channel 2 to Channel 1 [log (base 2) (RAT2N_MEDIAN)]
PIX_RAT2_MEAN Geometric mean of the pixel-by-pixel ratios of Channel 2 to Channel 1 pixel intensities, with the median background subtracted
PIX_RAT2_MEDIAN Median of pixel by-pixel ratios of Channel 2 to Channel 1 pixel intensities, with the median background subtracted
PERGTBCH1I_1SD Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 1
PERGTBCH1I_2SD
PERGTBCH2I_1SD Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 2
PERGTBCH2I_2SD Percentage of spot pixels with intensities more than two standard deviations above the background pixel intensity, at Channel 1
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio
RAT1N_MEAN Ratio of the means of Channel 1 intensity to normalized Channel 2 intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized
RAT2_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 2/Channel 1 ratio, (CH2I_MEAN - CH2B_MEDIAN)/(CH1_MEAN - CH1B_MEDIAN) or Red/Green ratio
RAT2_MEDIAN Ratio of the median intensities of each spot for each wavelength, with the median background subtracted
RAT2_SD Standard deviation of pixel intensity ratios
RAT2N_MEAN Channel 2/Channel 1 ratio normalized, RAT2N_MEAN/Normalization factor or Red/Green mean ratio normalized
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2N_MEDIAN/Normalization factor or Red/Green median ratio normalized
REGR Regression ratio
SUM_MEAN Sum of the arithmetic mean intensities for each wavelength, with the median background subtracted (CH1D_MEAN + CH2D_MEAN)
SUM_MEDIAN Sum of the median intensities for each wavelength, with the median-background subtracted (CH1D_MEDIAN + CH2D_MEDIAN)
TOT_BPIX Total number of background pixels
TOT_SPIX Total number of signal (spot) pixels
X_COORD X-coordinate in �m of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image
Y_COORD Y-coordinate in �m of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize)
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize)
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize)
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize)
UNF_VALUE aka LOG_RAT2N_MEAN, or Log (base 2) of the ratio of the mean of Channel 2 to Channel 1 [log (base 2) (RAT2N_MEAN)]

Data table
ID_REF CH1D_MEDIAN CH1I_MEDIAN CH1_PER_SAT CH1I_SD CH1B_MEAN CH1B_MEDIAN CH1B_SD CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2D_MEDIAN CH2I_MEDIAN CH2_PER_SAT CH2I_SD CH2B_MEAN CH2B_MEDIAN CH2B_SD CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN CH2DN_MEDIAN CH2IN_MEDIAN CORR DIAMETER FLAG VALUE LOG_RAT2N_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH1I_2SD PERGTBCH2I_1SD PERGTBCH2I_2SD RAT1_MEAN RAT1N_MEAN RAT2_MEAN RAT2_MEDIAN RAT2_SD RAT2N_MEAN RAT2N_MEDIAN REGR SUM_MEAN SUM_MEDIAN TOT_BPIX TOT_SPIX X_COORD Y_COORD TOP BOT LEFT RIGHT UNF_VALUE
1 572 692 0 245 120 120 40 595 796 670 693 819 0 254 126 126 46 173 918 1090 949 1122 .91 60 0 .625 .731 1.114 1.042 96 96 100 100 .888 .648 1.126 1.212 1.375 1.543 1.66 1.128 1265 1265 164 32 1560 9030 24 30 25 31 .625
2 4359 4462 0 2190 135 103 299 4453 19689 19574 18005 18120 0 8298 310 115 1613 158 26814 26971 24664 24822 .98 70 0 2.59 2.5 4.65 4.355 100 96 100 100 .227 .166 4.396 4.131 1.263 6.021 5.658 4.426 24027 22364 231 32 1710 9020 22 29 39 46 2.59
3 2658 2760 0 1576 108 102 57 2552 1623 1521 1567 1669 0 626 113 102 55 140 2084 2223 2147 2286 .95 50 0 -.293 -.308 .728 .59 100 100 100 100 1.678 1.225 .596 .59 1.921 .816 .808 .52 4073 4225 104 12 1860 9020 23 28 55 60 -.293
4 952 1014 0 646 79 62 40 962 567 489 562 640 0 288 84 78 37 107 670 777 770 877 .93 70 0 -.522 -.306 .544 .497 84 84 87 84 1.967 1.436 .508 .59 1.45 .696 .809 .457 1451 1514 224 32 2000 9020 22 29 68 75 -.522
5 1758 1813 0 973 58 55 17 1543 1724 1662 1678 1740 0 917 69 62 32 85 2277 2362 2299 2384 .96 60 0 .561 .387 1.177 1.079 96 96 100 100 .928 .678 1.077 .954 1.654 1.476 1.308 .998 3205 3436 171 32 2160 9030 24 30 85 91 .561
6 1180 1235 0 618 84 55 144 999 737 664 691 764 0 351 93 73 89 100 910 1010 947 1047 .92 50 0 -.135 -.318 .978 .697 75 75 100 91 1.505 1.098 .665 .586 3.321 .91 .802 .561 1663 1871 104 12 2290 9030 24 29 98 103 -.135
7 1119 1235 0 1101 122 116 92 1307 2486 2384 1803 1905 0 1702 115 102 65 140 3266 3405 2470 2610 .97 80 0 1.321 1.142 2.417 1.905 86 80 100 100 .548 .4 1.824 1.611 1.943 2.499 2.207 1.711 3691 2922 288 52 2450 9030 23 31 113 121 1.321
8 779 910 0 348 133 131 35 705 321 209 213 325 0 131 120 112 44 153 286 440 292 445 .8 60 0 -1.3 -1.417 .289 .325 96 93 93 81 3.373 2.462 .296 .273 2.004 .406 .375 .265 914 992 164 32 2590 9030 24 30 128 134 -1.3
9 505 630 0 251 129 125 34 474 1685 1569 1666 1782 0 631 120 116 40 159 2149 2308 2282 2441 .93 90 0 2.181 2.176 3.539 3.347 92 90 100 100 .302 .221 3.31 3.299 1.559 4.534 4.519 3.249 2043 2171 339 52 2730 9030 22 31 140 149 2.181
10 451 586 0 53 138 135 46 433 245 132 129 242 0 72 113 113 37 155 181 336 177 332 .74 50 0 -1.26 -1.352 .233 .301 100 100 91 83 3.28 2.395 .305 .286 2.642 .418 .392 .288 565 580 104 12 2880 9020 23 28 157 162 -1.26
11 6868 6997 0 2698 154 129 270 6132 658 545 596 709 0 253 117 113 41 155 747 901 816 971 .95 90 0 -3.038 -3.072 .092 .091 98 94 98 96 11.251 8.214 .089 .087 1.631 .122 .119 .085 6677 7464 358 52 3020 9020 21 30 169 178 -3.038
12 6744 6870 0 6256 151 126 262 8217 10144 10033 9342 9453 0 7447 119 111 44 152 13744 13896 12797 12949 .99 100 0 .742 .924 1.319 1.216 97 92 100 100 .819 .598 1.221 1.385 1.78 1.673 1.898 1.209 18250 16086 381 80 3180 9030 22 32 185 195 .742
13 1044 1175 0 831 135 131 36 1153 1321 1209 980 1092 0 885 115 112 38 153 1656 1810 1342 1496 .96 100 0 .522 .363 1.07 1.041 96 91 98 95 .954 .696 1.049 .939 1.803 1.436 1.286 1.057 2362 2024 354 80 3320 9030 22 32 199 209 .522
14 341 472 0 133 135 131 34 337 641 531 498 608 0 296 112 110 37 151 727 878 682 833 .83 110 0 1.11 1 1.505 1.552 100 97 100 100 .635 .463 1.576 1.46 1.589 2.158 2.001 1.881 868 839 422 80 3470 9030 21 32 213 224 1.11
15 1500 1630 0 626 136 130 47 1427 3411 3302 3581 3690 0 1196 125 109 140 149 4523 4673 4905 5055 .97 90 0 1.664 1.709 2.453 2.329 96 92 100 100 .432 .315 2.314 2.387 1.343 3.17 3.27 2.245 4729 5081 289 52 3610 9020 21 30 228 237 1.664
16 8671 8799 0 3959 133 128 48 8501 15016 14906 14463 14573 0 6115 123 110 117 151 20419 20570 19812 19963 .98 110 0 1.264 1.192 1.977 1.784 100 100 100 100 .57 .416 1.753 1.668 1.571 2.402 2.285 1.711 23407 23134 422 80 3760 9030 21 32 242 253 1.264
17 2473 2596 0 803 126 123 33 2347 22733 22623 25124 25234 0 7329 118 110 45 151 30990 31141 34416 34567 .97 110 0 3.723 3.799 9.908 9.684 100 100 100 100 .104 .076 9.639 10.159 1.317 13.204 13.917 9.662 24970 27597 383 80 3900 9030 21 32 256 267 3.723
18 1 123 0 127 126 122 33 29 133 24 1 110 0 79 116 109 46 149 33 182 1 151 .55 100 -50 .454 .814 .919 21 13 22 8 1.208 .882 .828 1 4.483 1.134 1.37 .658 53 2 339 80 4050 9020 21 31 272 282 .181
19 4563 4688 0 1971 128 125 38 4140 3078 2968 3388 3498 0 1212 123 110 77 151 4066 4216 4641 4792 .97 90 0 -.026 .024 .893 .751 98 96 100 100 1.395 1.018 .717 .742 2.351 .982 1.017 .684 7108 7951 261 52 4190 9030 22 31 286 295 -.026
20 2011 2135 0 1002 129 124 39 1873 2178 2069 2274 2383 0 849 121 109 67 149 2834 2984 3115 3264 .96 110 0 .598 .631 1.332 1.124 98 96 100 98 .905 .661 1.105 1.131 1.767 1.513 1.549 1.028 3942 4285 414 80 4340 9020 20 31 300 311 .598

Total number of rows: 43008

Table truncated, full table size 9334 Kbytes.




Supplementary data files not provided
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