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Sample GSM6267 Query DataSets for GSM6267
Status Public on Apr 15, 2004
Title AML 6
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 6
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=770650LaserPower=3.544.23
Lot batch = shcz076
 
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 GPL318
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
1 229 358 0 146 132 129 33 245 172 30 23 165 0 73 149 142 62 182 38 221 29 212 .2 90 0 -2.671 -2.957 .239 .227 94 94 26 13 8.167 6.37 .122 .1 3.32 .157 .129 .123 275 252 352 52 1780 7750 46 55 21 30 -2.671
2 2708 2836 0 1403 130 128 36 2673 541 389 365 517 0 213 161 152 76 195 499 694 468 663 .83 80 0 -2.422 -2.533 .147 .149 100 100 96 88 6.871 5.36 .146 .135 1.864 .187 .173 .129 3062 3073 254 52 1930 7750 47 55 37 45 -2.422
3 1576 1708 0 1094 136 132 36 1714 1246 1099 1030 1177 0 623 155 147 62 188 1409 1597 1321 1509 .9 90 0 -.283 -.255 .639 .627 100 100 98 98 1.56 1.216 .641 .654 2.063 .822 .838 .613 2813 2606 288 52 2070 7750 46 55 50 59 -.283
4 575 711 0 267 141 136 41 557 253 93 74 234 0 107 165 160 61 205 119 324 95 300 .38 80 0 -2.224 -2.6 .169 .182 100 98 55 28 5.989 4.672 .167 .129 3.343 .214 .165 .128 650 649 264 52 2220 7750 47 55 66 74 -2.224
5 323 460 0 130 141 137 36 328 504 347 305 462 0 192 160 157 59 201 445 646 391 592 .69 80 0 .44 .276 1.018 1.107 100 98 98 92 .945 .737 1.058 .944 1.915 1.356 1.211 1.197 675 628 255 52 2360 7750 47 55 80 88 .44
6 188 321 0 108 138 133 35 194 193 48 30 175 0 65 158 145 63 186 62 247 38 224 .15 80 0 -1.656 -2.289 .284 .403 94 90 38 13 4.042 3.153 .247 .16 3.726 .317 .205 .168 242 218 274 52 2510 7750 47 55 95 103 -1.656
7 456 584 0 224 138 128 87 483 1358 1213 1210 1355 0 469 153 145 61 186 1555 1741 1551 1737 .86 90 0 1.687 1.766 2.668 2.414 98 90 100 100 .398 .311 2.511 2.654 1.748 3.22 3.402 2.764 1696 1666 334 52 2660 7740 45 54 109 118 1.687
8 342 468 0 175 136 126 94 344 192 46 42 188 0 70 150 146 61 187 59 246 54 241 .28 80 0 -2.544 -2.667 .254 .237 90 82 40 19 7.478 5.833 .134 .123 2.299 .171 .157 .125 390 384 242 52 2810 7750 47 55 125 133 -2.544
9 109 237 0 65 131 128 33 116 209 66 49 192 0 93 149 143 65 183 85 268 63 246 .22 90 0 -.455 -.795 .704 .72 90 76 44 15 1.758 1.371 .569 .45 3.119 .729 .576 1.884 182 158 312 52 2950 7750 46 55 138 147 -.455
10 369 496 0 121 129 127 31 360 180 41 25 164 0 82 151 139 66 178 53 231 32 210 .17 80 0 -2.776 -3.525 .161 .17 100 98 28 13 8.78 6.849 .114 .068 2.94 .146 .087 .088 401 394 254 52 3100 7750 47 55 154 162 -2.776
11 550 684 0 395 137 134 36 613 282 132 111 261 0 124 158 150 63 192 169 362 142 335 .56 80 0 -1.857 -1.95 .223 .253 100 98 61 48 4.644 3.622 .215 .202 2.896 .276 .259 .171 745 661 282 52 3240 7750 47 55 168 176 -1.857
12 1449 1579 0 1201 143 130 160 1606 1175 1011 916 1080 0 591 173 164 72 210 1296 1506 1174 1385 .87 80 0 -.309 -.303 .733 .676 94 86 98 98 1.589 1.239 .63 .632 1.977 .807 .81 .545 2617 2365 254 52 3390 7750 47 55 183 191 -.309
13 393 526 0 297 138 133 37 433 835 674 586 747 0 432 165 161 65 206 864 1071 751 958 .83 90 0 .997 .935 1.504 1.552 98 96 98 96 .642 .501 1.557 1.491 2.47 1.996 1.912 1.534 1107 979 325 52 3530 7740 45 54 196 205 .997
14 92 232 0 66 148 140 46 97 282 117 110 275 0 108 174 165 70 212 150 362 141 353 .44 70 0 .629 .616 1.088 1.155 78 50 71 37 .829 .647 1.206 1.196 3.554 1.546 1.533 2.363 214 202 189 32 3690 7770 49 56 213 220 .629
15 179 315 0 107 147 136 51 176 10356 10197 10005 10164 0 4089 356 159 1423 204 13073 13277 12827 13031 .75 90 0 6.215 6.163 50.517 51.804 86 75 100 100 .017 .013 57.938 55.894 1.472 74.279 71.659 61.068 10373 10184 335 52 3830 7730 44 53 226 235 6.215
16 2703 2843 0 1966 145 140 40 2578 9122 8965 9347 9504 0 5823 266 157 1080 201 11494 11695 11983 12185 .93 100 0 2.157 2.148 3.972 3.458 97 97 95 85 .288 .224 3.478 3.458 2.143 4.458 4.433 3.457 11543 12050 383 80 3980 7750 46 56 241 251 2.157
17 628 764 0 377 142 136 72 595 1652 1499 1451 1604 0 800 163 153 66 196 1922 2118 1860 2056 .8 100 0 1.691 1.567 2.675 2.375 91 85 100 100 .397 .31 2.519 2.311 2.388 3.23 2.962 2.631 2094 2079 367 80 4130 7740 45 55 256 266 1.691
18 174 308 0 98 141 134 93 169 192 41 31 182 0 80 160 151 68 194 53 246 40 233 .27 70 0 -1.685 -2.13 .427 .395 81 43 43 12 4.122 3.215 .243 .178 4.834 .311 .228 .208 210 205 196 32 4260 7750 47 54 270 277 -1.685
19 538 668 0 212 134 130 41 547 248 104 103 247 0 94 148 144 59 185 133 318 132 317 .45 70 0 -2.037 -2.027 .172 .205 100 96 59 43 5.26 4.103 .19 .191 2.586 .244 .245 .173 651 641 228 32 4410 7740 46 53 285 292 -2.037
20 627 756 0 263 196 129 685 592 485 334 332 483 0 187 161 151 72 194 428 622 426 619 .77 70 0 -.467 -.559 .572 .633 34 0 93 84 1.772 1.383 .564 .53 2.009 .723 .679 .557 926 959 227 32 4550 7740 46 53 299 306 -.467

Total number of rows: 43008

Table truncated, full table size 9278 Kbytes.




Supplementary data files not provided
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