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Sample GSM6241 Query DataSets for GSM6241
Status Public on Apr 15, 2004
Title AML 82
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 82
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=670640LaserPower=44.48
Lot batch = shco033
 
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 95 292 0 66 212 197 61 101 223 47 43 219 0 50 181 176 54 160 43 203 39 199 .53 50 -100 -1.281 .312 .448 66 33 50 16 2.149 2.364 .465 .453 4.589 .423 .411 .566 148 138 99 12 1860 7820 75 80 63 68 -1.241
2 130 318 0 109 190 188 43 116 159 -11 -14 156 0 53 173 170 42 155 -10 145 142 .07 80 0 .361 .608 75 63 15 3 4.069 .05 105 116 262 52 1980 7830 75 83 74 82
3 1371 1561 0 594 192 190 42 1293 257 88 84 253 0 115 174 169 42 154 80 234 76 230 .45 100 0 -4.015 -4.166 .098 .08 97 97 62 50 14.693 16.163 .068 .061 3.521 .062 .056 .055 1381 1455 349 80 2140 7820 73 83 89 99 -4.015
4 1718 1911 0 1370 195 193 37 1843 1979 1805 1636 1810 0 1140 179 174 65 158 1641 1799 1487 1645 .96 100 0 -.168 -.208 1.171 .978 95 92 100 98 1.021 1.123 .979 .952 1.861 .89 .866 .908 3648 3354 317 80 2290 7830 74 84 104 114 -.168
5 234 433 0 248 209 199 60 270 451 270 293 474 0 241 208 181 250 165 245 410 266 431 .29 80 0 -.138 .187 .903 .954 76 71 55 19 1 1.1 1 1.252 1.854 .909 1.138 7.413 540 527 250 52 2440 7830 75 83 120 128 -.138
6 25 206 0 51 184 181 41 22 209 34 32 207 0 62 181 175 57 159 31 190 29 188 .26 100 -50 .219 1.177 1.053 33 11 33 6 .647 .712 1.545 1.28 3.558 1.405 1.164 1.664 56 57 354 80 2580 7810 72 82 133 143 .491
7 29 210 0 78 191 181 70 29 2048 1871 1638 1815 0 1056 200 177 112 161 1701 1862 1489 1650 .5 80 0 5.874 5.682 31.593 32.72 30 5 100 96 .015 .017 64.517 56.483 1.74 58.652 51.348 33.118 1900 1667 246 52 2730 7810 73 81 149 157 5.874
8 2292 2478 0 1750 194 186 68 2612 1859 1680 1473 1652 0 1006 184 179 53 163 1527 1690 1339 1502 .97 80 0 -.774 -.775 .776 .65 94 94 100 98 1.555 1.71 .643 .643 1.893 .585 .584 .608 4292 3765 231 52 2880 7820 74 82 164 172 -.774
9 223 404 0 165 182 181 38 204 2593 2423 2255 2425 0 1461 174 170 44 155 2203 2357 2050 2205 .87 110 0 3.433 3.201 11.476 11.274 81 75 100 100 .084 .093 11.877 10.112 1.82 10.798 9.193 11.883 2627 2478 369 80 3020 7820 72 83 176 187 3.433
10 0 182 0 73 185 182 35 7 189 10 8 187 0 68 180 179 46 163 9 172 7 170 .31 100 -50 .929 .959 30 15 28 13 .7 .77 1.429 3.219 1.299 1.266 17 8 332 80 3160 7810 72 82 191 201 .377
11 1148 1333 0 431 190 185 46 1113 572 398 409 583 0 168 176 174 46 158 362 520 372 530 .87 100 0 -1.621 -1.626 .372 .368 100 96 97 97 2.796 3.076 .358 .356 1.636 .325 .324 .323 1511 1557 368 80 3310 7820 73 83 206 216 -1.621
12 428 610 0 378 193 182 65 437 417 243 229 403 0 205 181 174 47 158 221 379 208 366 .86 90 0 -.984 -1.04 .578 .589 80 75 82 71 1.798 1.978 .556 .535 2.333 .506 .486 .515 680 657 306 52 3460 7830 74 83 221 230 -.984
13 209 392 0 190 206 183 87 205 255 68 62 249 0 93 189 187 51 170 62 232 56 226 .48 70 0 -1.73 -1.891 .394 .398 68 62 56 37 3.015 3.316 .332 .297 2.736 .302 .27 .259 273 271 183 32 3590 7830 75 82 235 242 -1.73
14 8 190 0 60 190 182 59 13 164 -8 -7 165 0 51 180 172 59 156 -7 149 150 .03 100 -50 .696 .692 21 5 10 0 3.295 2.21 5 1 400 80 3750 7810 72 82 250 260
15 1815 1992 0 1372 181 177 39 1978 667 501 407 573 0 357 175 166 59 151 455 606 370 521 .93 110 0 -2.119 -2.294 .287 .258 96 92 88 86 3.948 4.343 .253 .224 2.253 .23 .204 .242 2479 2222 397 80 3890 7820 72 83 263 274 -2.119
16 475 652 0 320 182 177 38 503 293 125 109 277 0 109 173 168 46 153 114 266 99 252 .75 100 0 -2.146 -2.261 .234 .233 91 87 77 56 4.024 4.426 .249 .229 2.597 .226 .209 .24 628 584 323 80 4040 7820 73 83 279 289 -2.146
17 15 188 0 70 179 173 36 22 175 14 13 174 0 65 165 161 43 146 13 159 12 158 .31 100 -50 -.344 .859 .881 37 21 28 12 1.571 1.729 .636 .867 3.44 .579 .788 .895 36 28 306 80 4190 7810 72 82 294 304 -.79
18 25 196 0 53 175 171 35 20 169 10 7 166 0 51 163 159 43 145 9 154 6 151 .22 100 -50 -1.974 .673 .754 38 18 17 6 2 2.2 .5 .28 3.27 .455 .255 1.76 30 32 301 80 4330 7810 72 82 308 318 -1.138
19 579 750 0 228 177 171 52 586 299 137 124 286 0 80 167 162 45 147 125 272 113 260 .72 110 0 -2.234 -2.361 .231 .243 97 97 90 71 4.277 4.705 .234 .214 1.717 .213 .195 .213 723 703 378 80 4480 7820 72 83 322 333 -2.234
20 306 477 0 177 178 171 53 274 636 468 498 666 0 224 169 168 45 153 425 578 453 605 .85 90 0 .635 .565 1.706 1.644 90 78 98 94 .585 .644 1.708 1.627 1.606 1.553 1.48 1.592 742 804 239 52 4620 7830 74 83 337 346 .635

Total number of rows: 43008

Table truncated, full table size 8881 Kbytes.




Supplementary data files not provided
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