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Sample GSM6337 Query DataSets for GSM6337
Status Public on Apr 15, 2004
Title AML 114
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 114
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=4.534.37
Lot batch = shdj104
 
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
1 487 627 0 248 141 140 29 495 644 537 510 617 0 283 110 107 33 115 577 692 548 663 .91 70 0 .222 .171 1.042 1.112 100 100 100 96 .922 .857 1.085 1.047 1.745 1.167 1.126 1.113 1032 997 212 32 1420 8700 22 29 18 25 .222
2 3278 3418 0 2662 143 140 30 3566 2703 2595 2248 2356 0 2145 111 108 33 116 2790 2906 2417 2533 .97 100 0 -.354 -.439 .658 .711 98 98 100 98 1.374 1.278 .728 .686 1.912 .782 .737 .756 6161 5526 401 80 1570 8700 21 31 32 42 -.354
3 1318 1458 0 803 143 140 29 1477 657 546 443 554 0 393 115 111 36 119 587 706 476 596 .96 70 0 -1.331 -1.468 .311 .367 100 100 96 96 2.705 2.516 .37 .336 1.689 .397 .361 .396 2023 1761 200 32 1720 8700 22 29 48 55 -1.331
4 556 693 0 503 139 137 29 692 446 335 271 382 0 255 113 111 34 119 360 480 291 411 .93 80 0 -.942 -.932 .488 .488 100 100 94 92 2.066 1.921 .484 .487 1.691 .521 .524 .475 1027 827 232 52 1860 8700 22 30 62 70 -.942
5 1741 1883 0 779 149 142 55 1611 1198 1081 1086 1203 0 619 123 117 45 126 1162 1288 1168 1294 .93 90 0 -.471 -.576 .616 .74 100 100 98 96 1.49 1.386 .671 .624 1.671 .722 .671 .685 2692 2827 322 52 2000 8690 20 29 75 84 -.471
6 1156 1302 0 446 149 146 46 996 850 726 750 874 0 375 127 124 43 133 781 914 806 940 .96 70 0 -.351 -.519 .689 .74 100 100 100 100 1.372 1.276 .729 .649 1.336 .784 .698 .74 1722 1906 219 32 2160 8690 21 28 92 99 -.351
7 2076 2216 0 1362 142 140 31 2006 2132 2012 2254 2374 0 1504 124 120 40 129 2163 2292 2424 2553 .96 80 0 .109 .223 .987 1.076 98 98 100 100 .997 .927 1.003 1.086 1.939 1.078 1.167 1.043 4018 4330 269 52 2300 8700 22 30 106 114 .109
8 924 1066 0 437 147 142 34 888 420 293 271 398 0 156 132 127 42 137 315 452 291 428 .9 70 0 -1.495 -1.665 .325 .31 100 100 90 90 3.031 2.819 .33 .293 1.962 .355 .315 .317 1181 1195 207 32 2440 8700 22 29 120 127 -1.495
9 575 714 0 296 142 139 34 584 644 521 494 617 0 318 127 123 39 132 560 692 531 663 .93 100 0 -.06 -.114 .827 .927 97 97 96 92 1.121 1.042 .892 .859 2.048 .959 .924 .939 1105 1069 395 80 2600 8690 20 30 135 145 -.06
10 515 663 0 200 149 148 32 489 411 286 298 423 0 168 127 125 38 134 308 442 320 455 .89 60 0 -.669 -.685 .514 .62 96 96 93 90 1.71 1.59 .585 .579 1.794 .629 .622 .62 775 813 138 32 2730 8700 23 29 150 156 -.669
11 5894 6038 0 3040 147 144 36 5390 822 695 606 733 0 433 128 127 38 137 747 884 652 788 .9 110 0 -2.851 -3.177 .133 .136 100 100 97 97 7.755 7.213 .129 .103 1.754 .139 .111 .121 6085 6500 435 80 2880 8700 20 31 162 173 -2.851
12 8189 8331 0 6195 145 142 32 8998 6841 6717 6099 6223 0 5030 126 124 36 133 7223 7356 6558 6691 .96 100 0 -.317 -.32 .743 .764 100 100 100 100 1.34 1.246 .746 .745 1.678 .803 .801 .767 15715 14288 365 80 3030 8700 21 31 178 188 -.317
13 1009 1146 0 708 138 137 30 1186 821 709 549 661 0 456 119 112 36 120 762 883 590 711 .95 100 0 -.638 -.773 .552 .594 100 100 100 96 1.673 1.556 .598 .544 1.572 .643 .585 .594 1895 1558 338 80 3180 8690 20 30 193 203 -.638
14 444 582 0 162 141 138 34 439 820 699 723 844 0 279 128 121 42 130 752 882 777 908 .91 110 0 .776 .808 1.491 1.577 100 100 98 98 .628 .584 1.592 1.628 1.871 1.712 1.751 1.653 1138 1167 410 80 3310 8690 19 30 205 216 .776
15 1382 1522 0 629 142 140 33 1386 2028 1897 1939 2070 0 917 134 131 42 141 2040 2181 2085 2226 .96 110 0 .557 .593 1.394 1.422 98 98 100 100 .731 .679 1.369 1.403 1.644 1.472 1.509 1.381 3283 3321 394 80 3470 8690 19 30 221 232 .557
16 8416 8553 0 4613 139 137 29 8475 14041 13912 14106 14235 0 8880 137 129 73 139 14959 15098 15168 15306 .96 120 0 .82 .85 1.565 1.638 98 98 100 98 .609 .567 1.642 1.676 1.978 1.765 1.802 1.769 22387 22522 428 120 3620 8700 20 32 236 248 .82
17 2950 3082 0 637 135 132 30 2811 41759 41634 45549 45674 0 8593 137 125 83 134 44768 44902 48977 49112 .96 110 0 3.993 4.053 15.026 15.074 100 100 100 100 .068 .063 14.811 15.44 1.273 15.926 16.603 15.149 44445 48499 352 80 3760 8690 19 30 250 261 3.993
18 17 149 0 216 134 132 29 91 174 57 38 155 0 98 122 117 41 126 61 187 41 167 .74 100 -50 1.265 .81 .816 41 27 45 18 1.596 1.485 .626 2.235 3.539 .674 2.404 .447 148 55 331 80 3910 8680 19 29 266 276 -.57
19 4835 4970 0 1704 135 135 29 4732 1845 1726 1851 1970 0 658 122 119 36 128 1856 1984 1990 2118 .96 110 0 -1.35 -1.281 .37 .359 100 100 100 100 2.742 2.55 .365 .383 1.556 .392 .412 .355 6458 6686 332 80 4050 8690 19 30 279 290 -1.35
20 2342 2477 0 986 137 135 29 2193 1900 1777 1795 1918 0 928 128 123 40 132 1911 2043 1930 2062 .96 120 0 -.199 -.279 .767 .792 99 98 99 98 1.234 1.148 .81 .766 1.622 .871 .824 .837 3970 4137 403 120 4200 8690 19 31 294 306 -.199

Total number of rows: 43008

Table truncated, full table size 9497 Kbytes.




Supplementary data files not provided
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