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Sample GSM6238 Query DataSets for GSM6238
Status Public on Apr 15, 2004
Title AML 103
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 103
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=690630LaserPower=3.974.46
Lot batch = shco030
 
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
1 175 348 0 140 183 173 57 128 228 21 28 235 0 87 211 207 60 505 51 556 68 573 .5 60 -100 -1.358 .464 .421 71 62 34 9 6.095 2.499 .164 .16 2.201 .4 .39 .613 149 203 161 32 1850 7660 59 65 62 68 -1.321
2 186 355 0 145 180 169 81 146 229 34 49 244 0 100 201 195 55 476 83 559 120 595 .44 80 -100 -.638 .515 .467 69 51 48 23 4.294 1.761 .233 .263 2.545 .568 .643 .421 180 235 271 52 1980 7690 61 69 74 82 -.816
3 1170 1327 0 645 164 157 50 1042 241 64 63 240 0 85 182 177 54 432 156 588 154 585 .47 100 0 -2.739 -2.929 .094 .091 93 92 53 33 16.281 6.675 .061 .054 3.004 .15 .131 .054 1106 1233 353 80 2130 7680 59 69 88 98 -2.739
4 2779 2943 0 1672 172 164 50 2331 757 572 549 734 0 415 190 185 54 451 1395 1846 1339 1790 .89 90 0 -.741 -1.053 .287 .251 90 84 88 84 4.075 1.671 .245 .198 2.344 .599 .482 .22 2903 3328 288 52 2290 7690 60 69 104 113 -.741
5 443 608 0 384 178 165 63 416 353 163 166 356 0 193 199 190 58 463 398 861 405 868 .78 70 0 -.065 -.13 .4 .459 71 71 59 56 2.552 1.046 .392 .375 2.873 .956 .914 .408 579 609 202 32 2440 7670 59 66 120 127 -.065
6 18 177 0 72 167 159 50 21 223 29 20 214 0 93 201 194 70 473 71 544 49 522 .4 100 -50 1.438 1.245 1.026 32 13 28 13 .724 .297 1.381 1.111 2.899 3.368 2.71 2.432 50 38 380 80 2570 7670 58 68 132 142 1.752
7 183 343 0 158 178 160 74 143 1349 1137 1192 1404 0 841 259 212 213 517 2773 3290 2907 3424 .78 70 0 4.277 3.99 5.708 5.533 65 59 81 71 .126 .052 7.951 6.514 2.527 19.393 15.887 7.07 1280 1375 210 32 2730 7660 58 65 149 156 4.277
8 2668 2838 0 2166 178 170 70 2575 910 715 639 834 0 556 208 195 77 476 1744 2220 1559 2034 .88 80 0 -.562 -.776 .368 .285 82 80 88 84 3.601 1.477 .278 .24 2.96 .677 .584 .232 3290 3307 206 52 2880 7690 61 69 164 172 -.562
9 453 610 0 349 164 157 62 450 1091 904 853 1040 0 618 191 187 57 456 2205 2661 2080 2537 .87 100 0 2.293 2.199 1.722 1.896 83 80 92 92 .498 .204 2.009 1.883 2.312 4.9 4.593 2.037 1354 1306 289 80 3010 7680 59 69 176 186 2.293
10 3 155 0 110 155 152 32 30 167 -19 -20 166 0 71 188 186 55 454 -46 407 405 .31 100 -50 .969 .942 35 26 13 5 3.209 .689 11 -17 332 80 3160 7670 58 68 191 201
11 850 1001 0 569 156 151 39 836 360 187 177 350 0 160 180 173 56 422 456 878 432 854 .74 100 0 -.874 -.977 .247 .234 92 92 80 67 4.471 1.833 .224 .208 2.528 .546 .508 .194 1023 1027 339 80 3310 7680 59 69 206 216 -.874
12 28 181 0 446 167 153 84 326 204 22 13 195 0 113 188 182 59 444 54 498 32 476 .53 60 0 -2.603 .179 .467 .552 46 46 31 18 14.818 6.075 .067 .464 4.469 .165 1.132 .174 348 41 164 32 3450 7670 60 66 222 228 -2.603
13 315 459 0 230 156 144 67 255 209 27 22 204 0 94 182 182 57 444 66 510 54 498 .48 70 0 -1.953 -2.553 .304 .289 68 68 37 18 9.444 3.872 .106 .07 2.315 .258 .17 .213 282 337 202 32 3590 7700 62 69 235 242 -1.953
14 33 173 0 70 145 140 41 25 153 -12 -4 161 0 54 171 165 53 402 -29 373 393 .25 100 -50 .695 .9 42 23 7 1 4.205 1.599 13 29 351 80 3750 7670 58 68 250 260
15 1736 1874 0 1329 152 138 69 1722 313 142 135 306 0 161 177 171 56 417 346 763 329 746 .71 100 0 -2.314 -2.398 .135 .113 85 85 72 55 12.127 4.972 .082 .078 3.112 .201 .19 .078 1864 1871 319 80 3890 7680 59 69 264 274 -2.314
16 642 793 0 402 197 151 178 571 272 91 95 276 0 102 186 181 58 441 222 663 232 673 .6 70 0 -1.363 -1.47 .197 .199 81 65 68 46 6.275 2.573 .159 .148 2.297 .389 .361 .14 662 737 194 32 4050 7660 58 65 281 288 -1.363
17 12 153 0 84 215 141 1174 29 171 -4 -17 158 0 71 370 175 2534 427 -10 417 385 .38 100 -50 .835 .955 0 0 0 0 4.151 63.869 25 -5 382 80 4190 7660 57 67 294 304
18 3 146 0 72 223 143 1298 11 290 114 -2 174 0 988 415 176 2807 429 278 707 424 .87 100 -50 1.345 1.136 0 0 1 1 .096 .04 10.364 4.287 25.277 2.194 125 1 311 80 4330 7660 57 67 308 318 4.66
19 431 576 0 223 154 145 52 402 283 108 112 287 0 103 176 175 50 427 263 690 273 700 .61 100 0 -.61 -.658 .323 .308 90 88 71 51 3.722 1.526 .269 .26 2.57 .655 .634 .252 510 543 373 80 4470 7680 59 69 322 332 -.61
20 418 575 0 284 186 157 110 350 473 294 336 515 0 210 188 179 62 437 717 1154 820 1256 .79 60 -100 .971 .902 .777 71 68 84 78 1.19 .488 .84 .804 1.866 2.049 1.961 .7 644 754 159 32 4640 7660 59 65 341 347 1.035

Total number of rows: 43008

Table truncated, full table size 8676 Kbytes.




Supplementary data files not provided
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