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Sample GSM6235 Query DataSets for GSM6235
Status Public on Apr 15, 2004
Title AML 17
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 17
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=650650LaserPower=4.144.45
Lot batch = shco027
 
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
1 192 508 0 211 314 316 57 235 1000 777 748 971 0 365 233 223 60 203 706 909 680 883 .81 80 0 1.588 1.824 4.208 3.459 76 65 100 98 .302 .333 3.306 3.896 2.192 3.006 3.542 2.919 1012 940 217 52 1840 7440 64 72 68 76 1.588
2 361 631 0 154 279 270 64 356 314 99 83 298 0 87 220 215 56 195 90 285 75 271 .58 90 0 -1.984 -2.258 .254 .256 98 92 69 36 3.596 3.956 .278 .23 2.418 .253 .209 .294 455 444 313 52 1970 7410 60 69 80 89 -1.984
3 2384 2641 0 1233 264 257 60 2388 398 199 171 370 0 147 203 199 49 181 181 362 155 336 .82 110 0 -3.722 -3.939 .081 .086 100 100 85 72 12 13.2 .083 .072 1.944 .076 .065 .081 2587 2555 429 80 2120 7410 59 70 94 105 -3.722
4 4290 4544 0 2982 264 254 70 4775 5156 4955 3873 4074 0 2948 204 201 57 183 4505 4687 3521 3704 .97 90 0 -.084 -.285 1.058 1.023 100 100 100 100 .964 1.06 1.038 .903 1.435 .943 .821 1.022 9730 8163 288 52 2270 7430 62 71 110 119 -.084
5 951 1229 0 580 284 278 61 952 682 476 445 651 0 293 211 206 50 187 433 620 405 592 .93 70 0 -1.138 -1.233 .503 .475 93 90 93 90 2 2.2 .5 .468 1.434 .455 .425 .469 1428 1396 225 32 2430 7420 62 69 127 134 -1.138
6 181 464 0 146 287 283 59 163 432 222 223 433 0 128 218 210 45 191 202 393 203 394 .7 60 0 .308 .164 1.261 1.035 68 68 90 84 .734 .808 1.362 1.232 1.949 1.238 1.12 1.051 385 404 150 32 2580 7420 63 69 143 149 .308
7 1169 1448 0 512 284 279 54 1053 363 154 133 342 0 119 215 209 50 190 140 330 121 311 .76 90 0 -2.911 -3.273 .142 .15 100 98 78 63 6.838 7.521 .146 .114 1.934 .133 .103 .149 1207 1302 326 52 2720 7420 61 70 155 164 -2.911
8 6065 6357 0 3831 293 292 54 5595 4085 3866 3835 4054 0 2483 223 219 54 199 3515 3714 3486 3685 .97 90 0 -.671 -.799 .803 .698 100 100 100 100 1.447 1.592 .691 .632 1.649 .628 .575 .669 9461 9900 315 52 2860 7420 61 70 169 178 -.671
9 884 1166 0 632 284 282 67 976 1585 1376 1295 1504 0 814 216 209 57 190 1251 1441 1177 1367 .95 100 0 .358 .413 1.508 1.396 96 95 100 100 .709 .78 1.41 1.465 1.679 1.282 1.332 1.382 2352 2179 383 80 3010 7420 61 71 184 194 .358
10 89 361 0 161 271 272 63 136 297 95 51 253 0 106 206 202 49 184 86 270 46 230 .67 100 -50 -.941 .661 .597 61 42 52 38 1.432 1.575 .699 .573 3.151 .635 .521 .586 231 140 328 80 3160 7410 60 70 199 209 -.655
11 1856 2143 0 961 287 287 65 2005 1513 1301 1178 1390 0 577 220 212 88 193 1183 1375 1071 1264 .95 110 0 -.761 -.793 .674 .685 100 100 100 100 1.541 1.695 .649 .635 1.421 .59 .577 .611 3306 3034 439 80 3290 7410 59 70 211 222 -.761
12 1277 1573 0 801 304 296 76 1320 1026 802 769 993 0 400 228 224 60 204 729 933 699 903 .95 70 0 -.856 -.869 .691 .604 93 93 100 96 1.646 1.81 .608 .602 1.676 .552 .547 .572 2122 2046 208 32 3450 7420 62 69 229 236 -.856
13 451 757 0 387 306 306 54 527 508 290 240 458 0 226 225 218 54 198 264 462 218 416 .89 100 0 -.999 -1.048 .51 .54 91 85 86 77 1.817 1.999 .55 .532 2.067 .5 .484 .532 817 691 345 80 3590 7420 61 71 242 252 -.999
14 62 370 0 126 307 308 62 79 284 61 48 271 0 84 229 223 61 203 55 258 44 246 .52 100 -50 -.507 .808 .689 48 27 41 22 1.295 1.425 .772 .774 3.241 .702 .704 .599 140 110 378 80 3750 7400 59 69 258 268 -.511
15 2613 2890 0 2843 288 277 158 3341 1341 1129 815 1027 0 905 217 212 63 193 1026 1219 741 934 .96 110 0 -1.703 -1.818 .392 .329 86 83 91 86 2.959 3.255 .338 .312 2.404 .307 .284 .316 4470 3428 394 80 3890 7420 60 71 271 282 -1.703
16 1233 1515 0 674 300 282 154 1271 718 504 466 680 0 272 219 214 60 195 458 653 424 618 .92 110 0 -1.472 -1.541 .391 .391 95 92 98 97 2.522 2.774 .397 .378 1.499 .36 .344 .375 1775 1699 440 80 4030 7410 59 70 285 296 -1.472
17 395 714 0 173 339 319 94 373 366 137 118 347 0 88 238 229 62 208 125 333 107 315 .61 50 0 -1.583 -1.881 .329 .381 91 83 83 50 2.723 2.995 .367 .299 2.159 .334 .272 .396 510 513 104 12 4200 7410 62 67 305 310 -1.583
18 132 436 0 128 299 304 65 103 468 229 257 496 0 157 248 239 67 217 208 425 234 451 .69 60 0 1.015 .824 1.903 1.742 62 50 81 68 .45 .495 2.223 1.947 2.046 2.021 1.77 1.639 332 389 136 32 4340 7420 63 69 319 325 1.015
19 1113 1387 0 509 277 274 80 1089 1328 1116 1034 1246 0 485 218 212 74 193 1015 1207 940 1133 .95 110 0 -.102 -.244 1.06 1.075 98 98 100 98 .976 1.073 1.025 .929 1.387 .932 .845 1.004 2205 2147 427 80 4470 7410 59 70 329 340 -.102
20 444 722 0 316 285 278 81 507 948 736 701 913 0 356 216 212 51 193 669 862 637 830 .9 100 0 .4 .521 1.446 1.414 90 88 97 97 .689 .758 1.452 1.579 1.921 1.32 1.435 1.344 1243 1145 397 80 4610 7410 60 70 344 354 .4

Total number of rows: 43008

Table truncated, full table size 9245 Kbytes.




Supplementary data files not provided
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