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Sample GSM6237 Query DataSets for GSM6237
Status Public on Apr 15, 2004
Title AML 77
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 77
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=700640LaserPower=3.974.42
Lot batch = shco029
 
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 GPL317
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
1 110 284 0 119 178 174 42 116 178 44 37 171 0 60 141 134 47 235 77 312 65 300 .33 90 0 -.588 -.761 .531 .501 71 61 48 25 2.636 1.503 .379 .336 3.348 .665 .59 .314 160 147 302 52 1840 7710 62 71 59 68 -.588
2 267 435 0 176 170 168 33 284 176 48 41 169 0 54 133 128 45 225 84 309 72 296 .45 100 0 -1.754 -1.892 .201 .206 93 90 47 22 5.917 3.373 .169 .154 2.535 .297 .269 .148 332 308 323 80 1990 7690 60 70 74 84 -1.754
3 2859 3031 0 969 181 172 72 2710 271 135 117 253 0 80 140 136 54 239 237 475 205 444 .7 110 0 -3.516 -3.8 .049 .05 100 100 87 53 20.074 11.442 .05 .041 1.862 .087 .072 .046 2845 2976 363 80 2130 7690 59 70 87 98 -3.516
4 3505 3677 0 2081 186 172 81 3569 1736 1604 1350 1482 0 943 139 132 53 232 2814 3046 2368 2600 .96 90 0 -.343 -.565 .448 .443 100 98 100 98 2.225 1.268 .449 .385 1.418 .788 .676 .436 5173 4855 291 52 2290 7700 61 70 104 113 -.343
5 746 935 0 460 193 189 55 687 473 340 413 546 0 260 142 133 45 233 596 830 725 958 .91 70 0 -.204 -.042 .376 .498 84 81 81 75 2.021 1.152 .495 .554 2.131 .868 .971 .484 1027 1159 192 32 2440 7690 61 68 120 127 -.204
6 31 214 0 81 184 183 40 43 179 38 24 165 0 63 164 141 117 247 67 314 42 289 .23 100 -50 .442 .831 .913 45 27 15 0 1.132 .645 .884 .774 2.427 1.55 1.358 3.837 81 55 373 80 2580 7680 59 69 133 143 .633
7 98 277 0 118 187 179 54 94 6038 5895 5494 5637 0 3817 202 143 280 251 10342 10593 9639 9889 .73 90 0 6.782 6.62 40.47 42.871 59 44 100 98 .016 .009 62.713 56.061 1.499 110.022 98.353 56.716 5989 5592 288 52 2730 7680 59 68 148 157 6.782
8 2560 2731 0 2708 179 171 65 3251 3377 3244 3177 3310 0 2401 160 133 140 233 5691 5925 5574 5807 .97 90 0 .808 1.122 1.214 .999 96 90 100 98 1.002 .571 .998 1.241 1.907 1.751 2.177 .952 6495 5737 264 52 2870 7680 59 68 162 171 .808
9 280 438 0 387 163 158 49 389 4497 4370 3650 3777 0 3292 139 127 106 223 7667 7889 6404 6626 .89 110 0 4.301 4.515 11.817 10.459 73 67 100 100 .089 .051 11.234 13.036 1.987 19.709 22.87 10.822 4759 3930 379 80 3010 7690 59 70 175 186 4.301
10 43 206 0 110 167 163 61 73 179 53 37 163 0 71 130 126 44 221 93 314 65 286 .45 100 -50 .594 .761 .691 40 26 47 27 1.377 .785 .726 .86 4.006 1.274 1.51 .619 126 80 323 80 3170 7680 59 69 192 202 .349
11 1465 1631 0 647 170 166 39 1383 410 281 285 414 0 157 136 129 44 226 493 719 500 726 .88 110 0 -1.488 -1.551 .182 .206 96 95 88 85 4.922 2.805 .203 .195 1.683 .356 .341 .185 1664 1750 379 80 3310 7690 59 70 205 216 -1.488
12 666 827 0 494 165 161 44 659 358 227 216 347 0 178 138 131 50 230 398 628 379 609 .8 70 0 -.727 -.814 .389 .34 84 78 78 75 2.903 1.655 .344 .324 3.398 .604 .569 .317 886 882 206 32 3470 7690 61 68 223 230 -.727
13 405 574 0 302 176 169 44 387 231 92 94 233 0 111 146 139 57 244 161 405 165 409 .65 80 0 -1.262 -1.296 .254 .287 84 80 57 34 4.207 2.398 .238 .232 2.97 .417 .407 .239 479 499 236 52 3610 7690 61 69 237 245 -1.262
14 4 170 0 78 171 166 40 17 130 0 -1 129 0 52 134 130 43 228 0 228 226 .21 100 -50 .905 .865 30 18 20 5 3.187 .487 17 3 294 80 3750 7670 58 68 250 260
15 1270 1432 0 1531 169 162 51 1640 736 611 505 630 0 498 129 125 43 219 1072 1291 886 1105 .89 120 0 -.613 -.52 .496 .378 92 88 93 87 2.684 1.53 .373 .398 3.082 .654 .698 .315 2251 1775 390 120 3890 7690 59 71 263 275 -.613
16 855 1017 0 523 171 162 53 761 375 248 232 359 0 182 132 127 51 223 435 658 407 630 .83 90 0 -.807 -1.071 .333 .339 92 88 80 75 3.069 1.749 .326 .271 1.833 .572 .476 .289 1009 1087 260 52 4050 7680 59 68 280 289 -.807
17 16 179 0 91 168 163 42 37 135 6 1 130 0 42 134 129 50 226 11 237 2 228 .05 100 -50 -3.189 .763 .6 36 27 13 3 6.167 3.515 .162 .063 3.243 .284 .11 .259 43 17 353 80 4190 7670 58 68 294 304 -1.814
18 14 173 0 71 164 159 41 33 150 21 25 154 0 50 133 129 45 226 37 263 44 270 .23 100 -50 1.647 .892 .685 41 25 30 7 1.571 .896 .636 1.786 3.146 1.116 3.133 .752 54 39 322 80 4340 7670 58 68 309 319 .159
19 659 821 0 265 169 162 45 653 246 113 108 241 0 75 139 133 46 233 198 432 189 423 .66 110 0 -1.72 -1.798 .16 .174 97 97 80 61 5.779 3.294 .173 .164 1.989 .304 .288 .157 766 767 400 80 4480 7680 58 69 322 333 -1.72
20 340 504 0 365 168 164 49 424 309 167 158 300 0 166 145 142 51 249 293 542 277 526 .76 80 0 -.533 -.295 .391 .462 80 76 65 57 2.539 1.447 .394 .465 2.631 .691 .815 .351 591 498 236 52 4630 7670 59 67 339 347 -.533

Total number of rows: 43008

Table truncated, full table size 8762 Kbytes.




Supplementary data files not provided
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