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Sample GSM6334 Query DataSets for GSM6334
Status Public on Apr 15, 2004
Title AML 98
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 98
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=4.664.29
Lot batch = shdj101
 
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
1 698 837 0 361 144 139 35 686 1543 1418 1478 1603 0 736 131 125 40 134 1525 1659 1589 1724 .96 90 0 1.152 1.187 2.111 2.091 100 100 100 100 .484 .45 2.067 2.117 1.293 2.223 2.277 2.122 2104 2176 321 52 1510 8770 20 29 18 27 1.152
2 4307 4450 0 2553 146 143 39 4064 647 518 536 665 0 355 133 129 40 139 557 696 576 715 .91 90 0 -2.867 -2.902 .139 .127 92 92 90 86 7.846 7.296 .127 .124 2.474 .137 .134 .121 4582 4843 306 52 1650 8780 21 30 32 41 -2.867
3 1513 1660 0 1420 148 147 37 2040 1139 1013 843 969 0 622 130 126 37 135 1089 1225 906 1042 .96 70 0 -.905 -.739 .528 .475 100 100 100 100 2.014 1.873 .497 .557 1.454 .534 .599 .458 3053 2356 225 32 1810 8770 21 28 49 56 -.905
4 1089 1233 0 537 152 144 47 1025 578 448 443 573 0 180 137 130 44 140 482 622 476 616 .91 60 0 -1.089 -1.193 .488 .424 100 96 100 100 2.288 2.128 .437 .407 1.744 .47 .437 .375 1473 1532 153 32 1960 8770 22 28 65 71 -1.089
5 1786 1926 0 984 144 140 33 1652 2239 2113 2382 2508 0 1132 129 126 35 135 2272 2408 2561 2697 .97 80 0 .46 .52 1.385 1.324 100 98 100 100 .782 .727 1.279 1.334 1.486 1.375 1.434 1.252 3765 4168 269 52 2090 8770 21 29 77 85 .46
6 1076 1217 0 480 145 141 36 1113 1101 975 937 1063 0 340 133 126 39 135 1048 1184 1008 1143 .92 70 0 -.086 -.095 .961 .888 100 100 100 100 1.142 1.062 .876 .871 1.737 .942 .936 .801 2088 2013 220 32 2240 8760 20 27 92 99 -.086
7 1536 1675 0 1182 142 139 31 1689 1737 1600 1372 1509 0 1131 140 137 40 147 1720 1868 1475 1623 .96 80 0 .027 -.058 .938 .945 100 100 100 96 1.056 .982 .947 .893 1.709 1.019 .96 .945 3289 2908 246 52 2380 8780 22 30 106 114 .027
8 1025 1164 0 557 145 139 38 952 487 354 356 489 0 244 135 133 37 143 381 524 383 526 .86 80 0 -1.323 -1.421 .348 .351 98 98 94 84 2.689 2.501 .372 .347 1.915 .4 .373 .355 1306 1381 254 52 2520 8770 21 29 120 128 -1.323
9 695 838 0 353 147 143 37 648 540 407 414 547 0 230 136 133 35 143 438 581 445 588 .93 100 0 -.566 -.643 .625 .631 97 95 98 92 1.592 1.481 .628 .596 1.833 .675 .641 .618 1055 1109 386 80 2680 8770 20 30 135 145 -.566
10 609 755 0 212 147 146 32 531 427 290 277 414 0 142 139 137 39 147 312 459 298 445 .85 70 0 -.768 -1.032 .524 .551 100 100 96 93 1.831 1.703 .546 .455 1.79 .587 .489 .525 821 886 192 32 2820 8760 20 27 150 157 -.768
11 7516 7658 0 2166 145 142 33 7247 1028 894 932 1066 0 344 137 134 40 144 961 1105 1002 1146 .94 90 0 -2.914 -2.907 .121 .122 100 100 100 100 8.106 7.539 .123 .124 1.423 .133 .133 .117 8141 8448 317 52 2960 8760 19 28 163 172 -2.914
12 7632 7773 0 6197 144 141 33 8918 9715 9584 8587 8718 0 6718 135 131 37 141 10305 10446 9233 9374 .98 100 0 .209 .275 1.079 1.051 100 100 100 100 .931 .865 1.075 1.125 1.495 1.156 1.21 1.078 18502 16219 340 80 3110 8770 20 30 178 188 .209
13 1080 1223 0 763 148 143 38 1242 3279 3147 2924 3056 0 2195 139 132 43 142 3384 3526 3144 3286 .95 110 0 1.446 1.542 2.385 2.598 98 98 100 100 .395 .367 2.534 2.707 1.94 2.725 2.911 2.755 4389 4004 351 80 3250 8770 19 30 191 202 1.446
14 481 624 0 241 148 143 37 509 872 737 657 792 0 349 143 135 81 145 792 938 706 852 .92 120 0 .639 .555 1.48 1.446 98 95 100 99 .691 .642 1.448 1.366 1.481 1.557 1.469 1.526 1246 1138 464 120 3400 8760 18 30 206 218 .639
15 1181 1327 0 584 149 146 35 1035 18911 18778 20726 20859 0 8296 136 133 39 143 20191 20334 22286 22429 .96 110 0 4.286 4.238 19.232 17.807 92 91 100 100 .055 .051 18.143 17.55 1.448 19.509 18.87 17.61 19813 21907 367 80 3550 8760 18 29 221 232 4.286
16 6746 6895 0 4178 151 149 42 7022 13799 13661 13511 13649 0 7817 146 138 49 148 14689 14838 14528 14676 .98 120 0 1.065 1.107 2.136 1.905 100 99 100 100 .514 .478 1.945 2.003 1.728 2.092 2.154 1.939 20683 20257 446 120 3700 8770 19 31 236 248 1.065
17 2478 2602 0 1025 127 124 106 2127 30658 30540 34861 34979 0 10823 123 118 59 127 32839 32966 37485 37612 .96 120 0 3.949 3.919 15.209 13.629 94 91 100 100 .07 .065 14.358 14.068 1.479 15.439 15.127 13.888 32667 37339 425 120 3850 8760 18 30 251 263 3.949
18 2 80 0 62 99 78 62 29 122 34 20 108 0 65 99 88 53 95 37 131 22 116 .61 100 -50 3.427 1.015 1.018 28 6 33 12 .853 .793 1.172 10 2.984 1.261 10.753 1.085 63 22 322 80 3990 8750 18 28 266 276 .334
19 3308 3442 0 1911 154 134 185 3444 2935 2814 3155 3276 0 1678 140 121 119 130 3026 3156 3392 3523 .97 100 0 -.187 .036 .89 .839 92 91 98 96 1.224 1.138 .817 .954 2.161 .879 1.026 .827 6258 6463 303 80 4140 8770 20 30 281 291 -.187
20 2202 2346 0 574 249 144 380 2026 2175 2043 2204 2336 0 722 209 132 286 142 2197 2339 2370 2512 .94 80 0 .117 .106 .956 1.054 98 98 96 94 .992 .922 1.008 1.001 1.472 1.084 1.076 1.036 4069 4406 258 52 4270 8750 19 27 295 303 .117

Total number of rows: 43008

Table truncated, full table size 9532 Kbytes.




Supplementary data files not provided
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