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Sample GSM6274 Query DataSets for GSM6274
Status Public on Apr 15, 2004
Title AML 69
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 69
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=680630LaserPower=4.014.72
Lot batch = shcz219
 
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 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 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
1 318 427 0 146 110 109 24 330 348 242 220 326 0 114 115 106 40 116 266 382 242 358 .84 80 0 -.311 -.395 .751 .674 100 96 100 96 1.364 1.241 .733 .692 1.776 .806 .76 .717 572 538 270 52 1890 7880 40 48 29 37 -.311
2 1304 1415 0 440 112 111 26 1264 387 271 274 390 0 132 121 116 40 127 298 425 301 429 .87 70 0 -2.086 -2.115 .192 .204 100 100 96 93 4.664 4.244 .214 .21 1.611 .236 .231 .216 1535 1578 213 32 2020 7870 39 46 42 49 -2.086
3 1843 1956 0 1075 113 113 27 1775 1063 946 951 1068 0 565 120 117 37 129 1040 1168 1045 1174 .96 80 0 -.772 -.818 .54 .547 100 100 98 98 1.876 1.707 .533 .516 1.638 .586 .567 .519 2721 2794 295 52 2180 7880 40 48 58 66 -.772
4 495 604 0 233 110 109 26 496 448 331 293 410 0 191 121 117 39 129 364 492 322 451 .88 90 0 -.447 -.62 .631 .647 98 98 98 92 1.498 1.364 .667 .592 1.875 .733 .65 .68 827 788 322 52 2330 7870 38 47 72 81 -.447
5 351 463 0 237 113 112 27 419 386 274 211 323 0 202 117 112 40 123 301 424 232 355 .86 90 0 -.477 -.598 .598 .589 98 96 98 90 1.529 1.392 .654 .601 1.757 .719 .661 .675 693 562 281 52 2470 7880 39 48 86 95 -.477
6 269 380 0 139 114 111 28 274 281 175 176 282 0 102 113 106 39 116 192 309 193 310 .82 60 0 -.511 -.476 .612 .694 93 90 90 84 1.566 1.425 .639 .654 1.56 .702 .719 .643 449 445 167 32 2620 7880 41 47 103 109 -.511
7 595 703 0 386 109 108 23 585 822 715 707 814 0 508 114 107 36 118 786 903 777 895 .96 80 0 .426 .385 1.238 1.265 96 96 98 96 .818 .745 1.222 1.188 1.461 1.343 1.306 1.261 1300 1302 272 52 2760 7870 39 47 116 124 .426
8 569 680 0 174 115 111 32 543 247 134 121 234 0 83 119 113 38 124 147 271 133 257 .74 70 0 -1.883 -2.097 .208 .238 100 96 90 75 4.052 3.688 .247 .213 2.038 .271 .234 .245 677 690 220 32 2900 7870 39 46 130 137 -1.883
9 356 470 0 145 116 114 34 356 292 180 179 291 0 111 118 112 40 123 198 321 197 320 .8 70 0 -.848 -.856 .457 .453 100 100 87 75 1.978 1.8 .506 .503 1.902 .556 .553 .527 536 535 227 32 3050 7870 39 46 145 152 -.848
10 361 475 0 142 115 114 29 357 196 84 92 204 0 64 116 112 37 123 92 215 101 224 .59 90 0 -1.951 -1.836 .225 .292 100 96 75 59 4.25 3.868 .235 .255 2.277 .259 .28 .228 441 453 338 52 3200 7880 39 48 159 168 -1.951
11 1208 1320 0 830 116 112 31 1119 422 311 284 395 0 231 118 111 38 122 342 464 312 434 .92 90 0 -1.711 -1.953 .303 .277 94 94 88 78 3.598 3.274 .278 .235 1.848 .305 .258 .264 1430 1492 314 52 3360 7860 37 46 175 184 -1.711
12 1110 1221 0 1406 113 111 24 1693 1313 1199 762 876 0 974 119 114 38 125 1318 1443 837 963 .98 80 0 -.362 -.407 .759 .725 100 100 100 100 1.412 1.285 .708 .686 1.455 .778 .754 .695 2892 1872 245 52 3490 7870 39 47 189 197 -.362
13 392 504 0 272 117 112 31 414 503 382 375 496 0 232 125 121 41 133 420 553 412 545 .91 60 0 .02 .072 .942 .98 90 90 90 90 1.084 .986 .923 .957 1.408 1.014 1.051 .846 796 767 165 32 3640 7870 40 46 205 211 .02
14 48 160 0 119 113 112 25 90 174 59 27 142 0 93 118 115 39 126 65 191 30 156 .69 100 -50 -.694 .856 .813 61 50 41 31 1.525 1.388 .656 .563 2.734 .72 .618 .793 149 75 388 80 3790 7860 37 47 218 228 -.473
15 1126 1239 0 439 114 113 24 1028 2370 2253 2392 2509 0 927 120 117 38 129 2476 2604 2629 2757 .97 90 0 1.268 1.223 2.245 2.2 100 100 100 100 .456 .415 2.192 2.124 1.356 2.408 2.334 2.236 3281 3518 300 52 3930 7870 38 47 232 241 1.268
16 4879 4988 0 2324 111 109 23 4510 8189 8074 8417 8532 0 3458 120 115 35 126 8873 8999 9249 9376 .97 90 0 .976 .923 2.038 1.855 100 100 100 100 .559 .508 1.79 1.725 1.487 1.967 1.896 1.719 12584 13296 325 52 4080 7860 37 46 247 256 .976
17 673 782 0 412 112 109 26 686 976 866 883 993 0 519 115 110 38 121 952 1073 970 1091 .94 100 0 .472 .528 1.204 1.276 98 97 100 98 .792 .721 1.262 1.312 1.628 1.387 1.442 1.275 1552 1556 405 80 4230 7870 38 48 262 272 .472
18 364 477 0 229 113 113 27 332 170 60 54 164 0 60 115 110 34 121 66 187 59 180 .55 60 0 -2.332 -2.617 .217 .223 90 90 68 40 5.533 5.035 .181 .148 2.209 .199 .163 .163 392 418 159 32 4370 7870 40 46 278 284 -2.332
19 633 744 0 754 114 111 28 844 998 884 547 661 0 775 119 114 41 125 971 1097 601 726 .97 80 0 .203 -.075 1.001 .992 94 92 98 94 .955 .869 1.047 .864 2.002 1.151 .95 1.035 1728 1180 274 52 4530 7850 37 45 293 301 .203
20 976 1090 0 669 117 114 31 1097 1574 1456 1119 1237 0 1049 123 118 38 130 1600 1730 1230 1359 .96 70 0 .545 .333 1.344 1.377 96 93 100 100 .753 .686 1.327 1.147 2.46 1.459 1.26 1.46 2553 2095 205 32 4660 7860 38 45 306 313 .545

Total number of rows: 43008

Table truncated, full table size 9422 Kbytes.




Supplementary data files not provided
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