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Sample GSM6314 Query DataSets for GSM6314
Status Public on Apr 15, 2004
Title AML 42
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 42
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=3.934.73
Lot batch = shdj081
 
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 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 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
1 381 503 0 233 126 122 42 394 1408 1270 1320 1458 0 632 144 138 53 122 1124 1246 1168 1290 .91 80 0 1.512 1.616 3.471 3.319 92 88 98 98 .31 .351 3.223 3.465 1.718 2.853 3.066 3.321 1664 1701 291 52 1740 8590 23 31 18 26 1.512
2 2825 2952 0 1578 133 127 44 3128 11739 11612 9782 9909 0 6034 136 127 49 112 10276 10388 8657 8769 .97 90 0 1.716 1.616 3.679 3.6 100 100 100 100 .269 .304 3.712 3.463 1.325 3.285 3.064 3.905 14740 12607 338 52 1890 8590 22 31 32 41 1.716
3 1474 1602 0 1062 130 128 34 1542 1425 1296 1216 1345 0 845 136 129 49 114 1147 1261 1076 1190 .97 60 0 -.427 -.454 .915 .884 100 96 100 100 1.19 1.344 .84 .825 1.504 .744 .73 .82 2838 2690 164 32 2030 8590 24 30 48 54 -.427
4 410 531 0 508 124 121 30 597 935 806 659 788 0 579 137 129 48 114 713 827 583 697 .95 80 0 .257 .508 1.592 1.468 96 92 98 94 .741 .837 1.35 1.607 1.701 1.195 1.422 1.249 1403 1069 263 52 2170 8590 23 31 61 69 .257
5 826 949 0 573 127 123 32 910 1742 1603 1425 1564 0 825 146 139 50 123 1419 1542 1261 1384 .96 80 0 .641 .61 2.054 1.77 98 98 100 100 .568 .641 1.762 1.725 1.763 1.559 1.527 1.671 2513 2251 287 52 2330 8590 23 31 77 85 .641
6 591 714 0 218 129 123 35 568 1360 1230 1126 1256 0 619 140 130 51 115 1088 1204 996 1112 .88 60 0 .938 .754 1.98 1.961 96 96 100 100 .462 .522 2.165 1.905 1.481 1.916 1.686 2.518 1798 1717 170 32 2470 8590 24 30 92 98 .938
7 1653 1779 0 806 148 126 142 1420 2880 2730 3194 3344 0 1270 199 150 290 133 2416 2549 2827 2959 .95 70 0 .767 .774 2.271 1.864 93 87 100 93 .52 .588 1.923 1.932 1.885 1.701 1.71 1.928 4150 4847 214 32 2610 8580 22 29 105 112 .767
8 580 705 0 240 127 125 34 580 441 311 269 399 0 134 136 130 52 115 275 390 238 353 .82 70 0 -1.075 -1.285 .539 .52 100 100 100 96 1.865 2.107 .536 .464 1.554 .475 .41 .502 891 849 226 32 2770 8590 23 30 121 128 -1.075
9 504 624 0 268 123 120 31 455 1305 1178 1349 1476 0 578 134 127 49 112 1042 1155 1194 1306 .92 90 0 1.196 1.244 2.963 2.609 88 86 100 98 .386 .436 2.589 2.677 1.725 2.291 2.369 2.579 1633 1853 340 52 2920 8590 22 31 135 144 1.196
10 380 507 0 80 134 127 45 388 365 233 229 361 0 66 142 132 56 117 206 323 203 319 .81 50 0 -.912 -.907 .591 .6 100 100 100 100 1.665 1.882 .601 .603 1.329 .531 .533 .654 621 609 98 12 3060 8580 23 28 151 156 -.912
11 5605 5732 0 2498 133 127 60 4697 757 617 614 754 0 382 150 140 58 124 546 670 543 667 .93 80 0 -3.105 -3.367 .156 .144 98 96 92 92 7.613 8.602 .131 .11 2.571 .116 .097 .132 5314 6219 288 52 3200 8580 22 30 164 172 -3.105
12 3713 3840 0 5154 131 127 54 6173 7561 7419 6587 6729 0 5293 149 142 57 126 6565 6691 5829 5955 .96 100 0 .089 .651 1.508 1.257 98 98 100 100 .832 .94 1.202 1.774 2.066 1.064 1.57 1.123 13592 10300 389 80 3360 8590 22 32 179 189 .089
13 1018 1143 0 589 127 125 31 959 1356 1224 1063 1195 0 740 137 132 46 117 1083 1200 941 1058 .93 100 0 .176 -.114 1.355 1.275 98 93 100 100 .783 .885 1.276 1.044 1.912 1.129 .924 1.283 2183 2081 343 80 3500 8590 22 32 193 203 .176
14 370 496 0 166 129 126 31 356 692 558 534 668 0 268 140 134 46 119 494 612 473 591 .84 110 0 .472 .353 1.583 1.58 96 96 98 96 .638 .721 1.567 1.443 1.523 1.387 1.277 1.528 914 904 371 80 3650 8590 21 32 207 218 .472
15 775 896 0 417 124 121 29 770 6418 6288 6565 6695 0 2735 134 130 46 115 5565 5680 5810 5925 .96 100 0 2.853 2.906 9.068 8.289 95 93 100 100 .122 .138 8.166 8.471 1.65 7.227 7.496 8.036 7058 7340 305 80 3790 8590 22 32 222 232 2.853
16 4037 4158 0 3109 126 121 34 4125 11841 11711 10688 10818 0 7931 136 130 49 115 10364 10479 9458 9573 .97 120 0 1.329 1.228 4.011 2.848 95 92 100 100 .352 .398 2.839 2.648 2.358 2.512 2.343 2.765 15836 14725 422 120 3940 8590 21 33 236 248 1.329
17 2071 2193 0 849 125 122 34 1735 48348 48217 54597 54728 16 17982 135 131 47 116 42670 42786 48316 48432 .95 120 0 4.62 4.544 28.17 26.873 99 97 100 100 .036 .041 27.791 26.363 1.437 24.594 23.33 27.351 49952 56668 377 120 4080 8590 21 33 250 262 4.62
18 21 143 0 51 125 122 33 29 169 39 21 151 0 78 134 130 47 115 35 150 19 134 .3 100 -50 -.176 1.459 1.453 38 22 36 16 .744 .84 1.345 1 3.191 1.19 .885 2.96 68 42 325 80 4220 8580 21 31 265 275 .251
19 3874 3996 0 1325 126 122 37 3601 2072 1943 2171 2300 0 692 136 129 53 114 1719 1834 1921 2035 .95 90 0 -1.066 -1.012 .546 .537 100 100 100 100 1.853 2.094 .54 .56 1.339 .477 .496 .517 5544 6045 268 52 4370 8580 21 30 280 289 -1.066
20 2068 2195 0 549 134 127 58 2049 1479 1341 1308 1446 0 429 151 138 85 122 1187 1309 1158 1280 .96 110 0 -.788 -.837 .644 .636 100 100 100 100 1.528 1.727 .654 .632 1.271 .579 .56 .651 3390 3376 417 80 4510 8580 20 31 293 304 -.788

Total number of rows: 43008

Table truncated, full table size 9478 Kbytes.




Supplementary data files not provided
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