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Sample GSM6229 Query DataSets for GSM6229
Status Public on Apr 15, 2004
Title AML 5
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 5
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=670650LaserPower=4.44.28
Lot batch = shco020
 
Submission date May 07, 2003
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
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 GPL317
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 µm 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 µm 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 µm 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
1 129 304 0 89 178 175 36 136 417 292 295 420 0 118 127 125 35 176 411 587 415 592 .72 90 0 1.596 1.687 2.425 2.088 88 73 100 98 .466 .331 2.147 2.287 2.467 3.024 3.221 2.121 428 424 320 52 1800 7470 78 87 59 68 1.596
2 254 421 0 81 169 167 36 265 184 57 58 185 0 42 128 127 34 179 80 259 82 261 .45 90 0 -1.723 -1.637 .192 .22 100 100 67 38 4.649 3.301 .215 .228 2.24 .303 .322 .181 322 312 290 52 1940 7470 78 87 73 82 -1.723
3 1962 2134 0 516 176 172 36 1914 270 145 145 270 0 68 125 125 36 176 204 380 204 380 .83 100 0 -3.228 -3.264 .073 .074 100 100 93 87 13.2 9.372 .076 .074 1.604 .107 .104 .076 2059 2107 393 80 2090 7460 77 87 88 98 -3.228
4 3299 3471 0 1685 174 172 33 3271 2690 2566 2571 2695 0 1369 125 124 35 175 3614 3789 3621 3796 .98 90 0 .144 .134 .788 .757 100 100 100 100 1.275 .905 .784 .779 1.29 1.105 1.098 .788 5837 5870 276 52 2230 7470 78 87 102 111 .144
5 362 536 0 289 174 174 33 401 381 259 186 308 0 186 126 122 38 172 365 537 262 434 .9 80 0 -.137 -.467 .66 .64 100 94 98 88 1.548 1.099 .646 .514 1.627 .91 .724 .616 660 548 253 52 2380 7470 79 87 118 126 -.137
6 125 299 0 69 178 174 35 133 224 99 87 212 0 54 128 125 37 176 139 315 123 299 .61 80 0 .068 -.029 .73 .704 94 86 90 59 1.343 .954 .744 .696 2.093 1.048 .98 .702 232 212 269 52 2530 7470 79 87 133 141 .068
7 580 754 0 179 175 174 34 556 563 440 427 550 0 130 126 123 32 173 620 793 601 775 .93 90 0 .157 .052 .807 .846 100 100 100 100 1.264 .897 .791 .736 1.331 1.115 1.037 .776 996 1007 306 52 2670 7470 78 87 146 155 .157
8 2489 2667 0 1516 180 178 35 2571 2239 2117 2205 2327 0 1082 127 122 35 172 2982 3154 3106 3277 .98 100 0 .214 .319 .912 .826 100 100 100 100 1.214 .862 .823 .886 1.478 1.16 1.248 .782 4688 4694 367 80 2820 7470 78 88 161 171 .214
9 424 600 0 290 176 176 35 443 3189 3064 2924 3049 0 1764 126 125 35 176 4315 4492 4118 4294 .96 100 0 3.284 3.28 7.738 6.701 93 88 100 100 .145 .103 6.916 6.896 1.68 9.742 9.713 6.817 3507 3348 365 80 2960 7470 78 88 175 185 3.284
10 280 463 0 60 183 183 41 284 285 156 147 276 0 68 129 129 35 182 220 401 207 389 .75 50 0 -.37 -.436 .518 .596 100 100 100 100 1.821 1.293 .549 .525 1.59 .774 .739 .633 440 427 104 12 3110 7460 79 84 192 197 -.37
11 1457 1633 0 378 177 176 36 1451 780 653 641 768 0 154 129 127 35 179 920 1099 903 1082 .95 110 0 -.658 -.69 .454 .447 100 100 100 100 2.222 1.578 .45 .44 1.25 .634 .62 .437 2104 2098 448 80 3260 7460 76 87 204 215 -.658
12 644 809 0 204 169 165 34 651 378 256 245 367 0 90 125 122 34 172 361 532 345 517 .88 80 0 -.852 -.9 .389 .381 100 100 100 98 2.543 1.806 .393 .38 1.403 .554 .536 .377 907 889 242 52 3400 7460 78 86 220 228 -.852
13 465 632 0 189 168 167 32 459 478 357 360 481 0 148 123 121 33 170 503 673 507 677 .91 80 0 .132 .125 .798 .79 100 100 100 100 1.286 .913 .778 .774 1.529 1.095 1.09 .776 816 825 242 52 3550 7470 79 87 235 243 .132
14 170 334 0 75 161 164 31 168 195 80 78 193 0 50 116 115 33 162 113 275 110 272 .53 60 0 -.576 -.63 .427 .427 96 93 71 59 2.1 1.491 .476 .459 2.561 .671 .646 .373 248 248 152 32 3690 7470 80 86 250 256 -.576
15 2180 2341 0 1267 162 161 33 2247 927 810 801 918 0 378 121 117 34 165 1141 1306 1128 1293 .97 100 0 -.978 -.95 .388 .379 100 100 100 100 2.774 1.97 .36 .367 1.385 .508 .518 .334 3057 2981 411 80 3840 7470 78 88 263 273 -.978
16 903 1069 0 217 168 166 34 870 711 597 579 693 0 125 118 114 32 161 841 1001 815 976 .95 90 0 -.049 -.147 .696 .669 100 100 100 100 1.457 1.035 .686 .641 1.262 .966 .903 .665 1467 1482 321 52 3990 7460 77 86 278 287 -.049
17 213 393 0 71 180 180 32 216 221 99 82 204 0 59 125 122 34 172 139 311 115 287 .59 70 0 -.631 -.883 .396 .374 100 100 90 65 2.182 1.549 .458 .385 2.183 .646 .542 .406 315 295 206 32 4130 7460 78 85 293 300 -.631
18 88 252 0 79 168 164 35 108 2172 2045 2085 2212 0 619 128 127 37 179 2880 3059 2937 3115 .64 90 0 4.737 5.061 21.047 20.328 82 59 100 100 .053 .037 18.935 23.693 1.944 26.669 33.371 21.678 2153 2173 328 52 4280 7460 77 86 307 316 4.737
19 732 900 0 200 171 168 34 763 870 742 752 880 0 199 130 128 36 180 1045 1225 1059 1239 .94 110 0 .454 .533 .971 .991 100 100 100 100 1.028 .73 .972 1.027 1.319 1.37 1.447 .995 1505 1484 403 80 4430 7460 76 87 321 332 .454
20 367 531 0 147 167 164 37 393 251 132 128 247 0 70 123 119 34 168 186 354 180 348 .81 90 0 -1.08 -1.026 .304 .314 100 98 94 82 2.977 2.114 .336 .349 1.697 .473 .491 .336 525 495 262 52 4580 7460 77 86 337 346 -1.08

Total number of rows: 43008

Table truncated, full table size 9244 Kbytes.




Supplementary data files not provided
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