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Sample GSM6343 Query DataSets for GSM6343
Status Public on Apr 15, 2004
Title AML 51
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 51
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix Pro
Software version: 3.0.6.81
Scanning parameters: PMTVolts=770610LaserPower=3.564.65
Lot batch = shdj110
 
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
1 549 681 0 122 147 132 53 547 457 236 229 450 0 125 231 221 91 238 254 491 246 484 .66 50 0 -1.108 -1.157 .377 .433 100 100 83 66 2.318 2.156 .431 .417 1.865 .464 .449 .498 783 778 104 12 1610 8660 27 32 18 23 -1.108
2 2523 2670 0 645 208 147 248 2448 626 404 397 619 0 156 236 222 109 239 434 673 427 666 .82 50 0 -2.494 -2.563 .159 .171 100 100 100 91 6.059 5.635 .165 .157 1.628 .177 .169 .167 2852 2920 104 12 1750 8650 26 31 32 37 -2.494
3 3306 3443 0 1976 155 137 69 2782 1274 1044 1194 1424 0 713 236 230 85 247 1123 1370 1284 1531 .95 50 0 -1.309 -1.365 .407 .362 100 100 100 100 2.665 2.478 .375 .361 1.413 .404 .388 .347 3826 4500 104 12 1890 8660 27 32 46 51 -1.309
4 680 816 0 179 148 136 47 646 527 307 287 507 0 140 232 220 92 237 330 567 309 545 .72 50 0 -.969 -1.14 .45 .445 100 100 100 83 2.104 1.957 .475 .422 1.819 .511 .454 .549 953 967 104 12 2050 8660 27 32 62 67 -.969
5 1681 1818 0 946 187 137 277 1636 1566 1346 1122 1342 0 890 275 220 242 237 1447 1684 1206 1443 .94 60 0 -.177 -.479 .844 .827 87 81 87 81 1.215 1.13 .823 .667 1.977 .885 .718 .806 2982 2803 172 32 2170 8660 27 33 74 80 -.177
6 474 611 0 69 151 137 67 470 381 185 167 363 0 103 211 196 97 211 199 410 180 390 .61 50 0 -1.24 -1.4 .335 .395 100 100 75 41 2.541 2.363 .394 .352 1.864 .423 .379 .464 655 641 104 12 2330 8650 26 31 90 95 -1.24
7 1638 1783 0 1080 235 145 407 1688 4913 4670 4609 4852 0 2788 485 243 984 261 5022 5283 4956 5217 .97 50 0 1.573 1.597 2.763 2.899 83 75 91 75 .361 .336 2.767 2.814 1.322 2.975 3.026 2.601 6358 6247 104 12 2470 8650 26 31 104 109 1.573
8 1004 1145 0 483 141 141 31 983 326 118 92 300 0 123 221 208 88 224 127 351 99 323 .54 60 0 -2.954 -3.343 .173 .168 96 96 50 37 8.331 7.747 .12 .092 3.28 .129 .099 .125 1101 1096 176 32 2630 8660 27 33 120 126 -2.954
9 960 1098 0 328 157 138 81 895 619 396 431 654 0 252 243 223 105 240 426 666 463 703 .79 60 0 -1.072 -1.051 .402 .461 93 93 84 71 2.26 2.102 .442 .449 2.462 .476 .483 .492 1291 1391 170 32 2770 8660 27 33 134 140 -1.072
10 475 627 0 76 169 152 69 474 357 115 72 314 0 107 240 242 89 260 124 384 77 338 .57 50 0 -1.939 -2.617 .183 .174 100 100 41 33 4.122 3.833 .243 .152 2.604 .261 .163 .364 589 547 104 12 2920 8650 26 31 149 154 -1.939
11 6130 6262 0 3944 135 132 46 6205 766 554 512 724 0 419 225 212 94 228 596 824 551 778 .9 100 0 -3.381 -3.477 .091 .093 100 98 87 77 11.2 10.416 .089 .084 2.04 .096 .09 .087 6759 6642 437 80 3070 8660 25 35 162 172 -3.381
12 13075 13207 0 9037 137 132 35 12818 8302 8087 7430 7645 0 5591 232 215 93 231 8696 8927 7989 8220 .98 90 0 -.56 -.711 .704 .646 100 98 98 98 1.585 1.474 .631 .568 1.641 .678 .611 .614 20905 20505 292 52 3220 8660 25 34 177 186 -.56
13 867 996 0 521 134 129 33 826 1013 806 787 994 0 550 213 207 82 223 867 1089 846 1069 .94 100 0 .069 -.035 .884 .939 96 93 91 83 1.025 .953 .976 .908 1.812 1.049 .976 1.028 1632 1654 331 80 3360 8660 25 35 191 201 .069
14 869 998 0 504 135 129 38 929 411 196 167 382 0 172 223 215 89 231 211 442 180 411 .66 120 0 -2.14 -2.275 .202 .207 99 98 72 45 4.74 4.408 .211 .192 2.07 .227 .207 .202 1125 1036 461 120 3500 8660 24 36 204 216 -2.14
15 2398 2531 0 728 186 133 299 2203 3924 3708 4071 4287 0 1070 303 216 475 232 3987 4219 4377 4610 .97 90 0 .856 .868 1.723 1.702 98 94 98 96 .594 .553 1.683 1.698 1.26 1.81 1.825 1.69 5911 6469 274 52 3640 8650 24 33 219 228 .856
16 10696 10829 0 7830 163 133 224 11628 21103 20899 19861 20065 0 14087 258 204 360 219 22472 22691 21356 21575 .98 120 0 .951 .998 1.748 1.781 97 97 97 95 .556 .517 1.797 1.857 1.547 1.933 1.997 1.813 32527 30557 497 120 3800 8660 24 36 234 246 .951
17 2527 2659 0 846 144 132 90 2288 5392 5195 5819 6016 0 1987 211 197 95 212 5586 5798 6257 6469 .97 120 0 1.288 1.308 2.345 2.319 98 98 100 100 .44 .41 2.271 2.303 1.603 2.441 2.476 2.324 7483 8346 445 120 3950 8660 24 36 249 261 1.288
18 26 155 0 172 132 129 32 85 286 96 70 260 0 135 197 190 77 204 103 308 75 280 .47 100 -50 1.534 1.543 1.552 43 28 47 23 .885 .823 1.129 2.692 3.196 1.214 2.895 1.034 181 96 328 80 4090 8650 24 34 264 274 .28
19 5634 5767 0 1302 181 133 298 5365 2678 2467 2534 2745 0 635 235 211 147 227 2653 2880 2725 2952 .97 90 0 -1.016 -1.048 .459 .462 100 100 100 100 2.175 2.022 .46 .45 1.224 .494 .484 .442 7832 8168 272 52 4230 8650 24 33 278 287 -1.016
20 2407 2540 0 1043 247 133 1183 2172 1895 1689 1854 2060 0 916 266 206 526 222 1816 2038 1994 2215 .89 120 0 -.258 -.272 .755 .788 79 50 83 72 1.286 1.196 .778 .77 1.539 .836 .828 .771 3861 4261 480 120 4390 8660 24 36 293 305 -.258

Total number of rows: 43008

Table truncated, full table size 9278 Kbytes.




Supplementary data files not provided
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