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Sample GSM6315 Query DataSets for GSM6315
Status Public on Apr 15, 2004
Title AML 93
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 93
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=660650LaserPower=3.924.73
Lot batch = shdj082
 
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
1 310 423 0 127 114 113 30 313 1051 953 979 1077 0 447 113 98 97 102 993 1095 1020 1122 .88 70 0 1.665 1.718 2.868 2.935 100 100 100 96 .328 .315 3.045 3.158 1.649 3.172 3.29 3.536 1266 1289 224 32 1770 8250 29 36 17 24 1.665
2 3285 3397 0 1632 114 112 30 3459 1325 1234 1345 1436 0 621 104 91 73 95 1285 1380 1401 1496 .94 90 0 -1.428 -1.229 .341 .355 100 100 100 98 2.803 2.691 .357 .409 1.696 .372 .426 .34 4693 4630 349 52 1930 8250 28 37 32 41 -1.428
3 872 986 0 472 119 114 30 899 712 616 615 711 0 328 100 96 35 100 642 742 641 741 .91 70 0 -.486 -.445 .676 .709 100 96 100 100 1.459 1.401 .685 .705 1.738 .714 .735 .666 1515 1487 215 32 2070 8250 29 36 47 54 -.486
4 588 698 0 315 112 110 25 542 513 414 336 435 0 277 100 99 32 103 431 534 350 453 .9 70 0 -.33 -.748 .789 .792 100 96 100 100 1.309 1.257 .764 .571 1.81 .796 .595 .793 956 924 206 32 2210 8250 29 36 61 68 -.33
5 788 902 0 442 114 114 26 834 683 584 576 675 0 331 102 99 32 103 608 711 600 703 .92 90 0 -.455 -.393 .666 .714 98 98 96 92 1.428 1.371 .7 .731 1.68 .729 .761 .699 1418 1364 328 52 2360 8250 28 37 75 84 -.455
6 610 725 0 197 116 115 26 597 516 419 377 474 0 246 102 97 33 101 436 538 393 494 .86 70 0 -.452 -.635 .636 .658 100 100 100 100 1.425 1.368 .702 .618 1.648 .731 .644 .752 1016 987 207 32 2500 8260 30 37 90 97 -.452
7 977 1091 0 606 115 114 26 946 1887 1793 1906 2000 0 1150 97 94 32 98 1868 1966 1985 2083 .93 90 0 .981 1.023 1.848 1.986 98 96 100 98 .528 .507 1.895 1.951 2.15 1.974 2.032 1.985 2739 2883 325 52 2650 8250 28 37 104 113 .981
8 413 531 0 228 118 118 26 420 200 104 95 191 0 68 100 96 33 100 108 208 99 199 .75 80 0 -1.955 -2.061 .244 .266 100 96 84 67 4.038 3.877 .248 .23 2.089 .258 .24 .221 524 508 267 52 2790 8250 29 37 119 127 -1.955
9 329 445 0 128 119 116 33 326 679 578 570 671 0 291 104 101 35 105 602 707 594 699 .88 80 0 .885 .852 1.601 1.853 98 98 96 96 .564 .541 1.773 1.733 1.696 1.847 1.805 2.024 904 899 274 52 2940 8250 29 37 134 142 .885
10 230 341 0 92 116 111 29 240 198 96 93 195 0 47 106 102 36 106 100 206 97 203 .63 60 0 -1.263 -1.247 .365 .427 96 96 96 59 2.5 2.4 .4 .404 1.936 .417 .421 .377 336 323 170 32 3090 8250 30 36 150 156 -1.263
11 4146 4261 0 1619 120 115 28 4318 485 382 380 483 0 204 111 103 40 107 398 505 396 503 .89 80 0 -3.44 -3.389 .081 .092 100 100 100 96 11.304 10.852 .088 .092 1.835 .092 .095 .083 4700 4526 278 52 3230 8250 29 37 163 171 -3.44
12 7394 7507 0 3097 118 113 29 7158 8050 7945 8745 8850 0 3189 110 105 37 109 8276 8385 9109 9219 .95 90 0 .209 .301 1.137 1.114 100 100 100 100 .901 .865 1.11 1.183 1.483 1.156 1.232 1.1 15103 16139 316 52 3380 8250 28 37 177 186 .209
13 844 960 0 453 120 116 29 925 1083 981 882 984 0 533 106 102 36 106 1022 1128 919 1025 .9 90 0 .144 .122 1.045 1.091 100 100 100 100 .943 .905 1.061 1.045 1.635 1.105 1.089 1.026 1906 1726 300 52 3520 8250 28 37 191 200 .144
14 269 389 0 113 123 120 29 272 517 416 404 505 0 210 107 101 36 105 433 539 421 526 .86 110 0 .672 .646 1.396 1.524 98 97 98 96 .654 .628 1.529 1.502 1.867 1.593 1.564 1.754 688 673 459 80 3670 8250 27 38 205 216 .672
15 464 579 0 206 119 115 30 441 3974 3870 4075 4179 0 1387 111 104 38 108 4031 4140 4245 4353 .89 90 0 3.192 3.193 9.512 8.099 94 94 100 100 .114 .109 8.776 8.782 1.887 9.141 9.148 9.106 4311 4539 301 52 3820 8250 28 37 221 230 3.192
16 5271 5387 0 2546 119 116 30 5413 10952 10848 10803 10907 0 4610 110 104 43 108 11300 11408 11253 11361 .95 110 0 1.062 1.094 2.094 2.008 100 100 100 100 .499 .479 2.004 2.05 1.503 2.088 2.135 1.977 16261 16074 396 80 3970 8260 28 39 235 246 1.062
17 1598 1711 0 660 117 113 28 1413 20458 20357 23880 23981 0 9180 105 101 36 105 21205 21310 24875 24980 .95 120 0 3.908 3.96 14.586 14.734 98 95 100 100 .069 .067 14.407 14.944 1.632 15.007 15.566 14.98 21770 25478 416 120 4110 8260 28 40 249 261 3.908
18 10 126 0 85 119 116 30 31 140 39 24 125 0 83 106 101 36 105 41 146 25 130 .64 100 -50 1.322 1.7 1.083 25 13 35 22 .795 .763 1.258 2.4 3.6 1.31 2.5 1.024 70 34 307 80 4260 8250 28 38 265 275 .39
19 3437 3551 0 1242 118 114 30 3328 1961 1861 1877 1977 0 714 105 100 36 104 1939 2043 1955 2059 .95 90 0 -.78 -.814 .572 .561 100 100 100 100 1.788 1.717 .559 .546 1.442 .582 .569 .547 5189 5314 246 52 4400 8250 28 37 279 288 -.78
20 1502 1616 0 848 117 114 33 1476 1167 1067 1102 1202 0 590 107 100 52 104 1111 1216 1148 1252 .94 120 0 -.409 -.388 .731 .735 97 96 95 94 1.383 1.328 .723 .734 2.026 .753 .764 .7 2543 2604 481 120 4550 8250 27 39 293 305 -.409

Total number of rows: 43008

Table truncated, full table size 9370 Kbytes.




Supplementary data files not provided
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