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Sample GSM6328 Query DataSets for GSM6328
Status Public on Apr 15, 2004
Title AML 90
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 90
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=730640LaserPower=4.414.53
Lot batch = shdj095
 
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
1 407 562 0 231 159 155 32 418 844 645 635 834 0 306 212 199 70 249 806 1055 794 1043 .91 70 0 .948 .964 1.598 1.524 96 93 96 93 .648 .518 1.543 1.56 1.545 1.929 1.95 1.524 1063 1042 210 32 1600 8360 20 27 20 27 .948
2 3664 3819 0 2134 157 155 30 3659 1485 1286 1315 1514 0 657 206 199 68 249 1608 1856 1644 1893 .96 80 0 -1.187 -1.156 .363 .356 100 100 100 98 2.845 2.276 .351 .359 1.469 .439 .449 .325 4945 4979 276 52 1750 8360 20 28 35 43 -1.187
3 1171 1324 0 849 157 153 28 1305 949 757 661 853 0 541 198 192 60 240 946 1186 826 1066 .96 60 0 -.464 -.503 .567 .615 100 96 96 90 1.724 1.379 .58 .564 1.521 .725 .706 .585 2062 1832 165 32 1890 8360 21 27 50 56 -.464
4 375 530 0 340 156 155 32 492 392 186 201 407 0 170 205 206 60 258 233 490 251 509 .75 60 0 -1.081 -.578 .402 .407 100 96 68 62 2.645 2.116 .378 .536 1.653 .473 .67 .372 678 576 156 32 2030 8360 21 27 64 70 -1.081
5 947 1098 0 616 154 151 30 1029 1492 1287 1058 1263 0 698 206 205 66 256 1609 1865 1323 1579 .96 90 0 .645 .482 1.317 1.285 100 100 100 100 .8 .64 1.251 1.117 1.438 1.563 1.397 1.228 2316 2005 317 52 2180 8360 19 28 77 86 .645
6 847 996 0 292 154 149 33 803 1141 950 892 1083 0 462 195 191 63 239 1188 1426 1115 1354 .93 70 0 .564 .397 1.109 1.163 100 100 100 100 .845 .676 1.183 1.053 1.454 1.479 1.316 1.326 1753 1739 213 32 2320 8350 19 26 92 99 .564
7 1626 1772 0 1025 148 146 30 1593 2461 2268 2509 2702 0 1258 198 193 60 241 2835 3076 3136 3378 .97 90 0 .832 .948 1.63 1.499 98 96 98 98 .702 .562 1.424 1.543 1.704 1.78 1.929 1.369 3861 4135 320 52 2470 8360 19 28 106 115 .832
8 521 671 0 261 163 150 76 590 420 219 233 434 0 117 210 201 78 251 274 525 291 543 .81 70 0 -1.108 -.839 .354 .4 100 100 90 71 2.694 2.155 .371 .447 1.911 .464 .559 .417 809 754 204 32 2600 8350 19 26 120 127 -1.108
9 547 700 0 248 160 153 58 512 1474 1283 1323 1514 0 551 199 191 72 239 1604 1843 1654 1893 .95 100 0 1.647 1.596 2.662 2.538 97 95 100 100 .399 .319 2.506 2.419 1.512 3.132 3.023 2.526 1795 1870 387 80 2770 8360 19 29 136 146 1.647
10 362 513 0 121 155 151 32 373 439 243 254 450 0 122 200 196 70 245 304 549 318 563 .72 60 0 -.296 -.189 .61 .717 100 100 90 78 1.535 1.228 .651 .702 1.872 .814 .877 .7 616 616 151 32 2900 8350 20 26 151 157 -.296
11 6145 6298 0 1949 152 153 32 5624 1191 996 1007 1202 0 403 198 195 64 244 1245 1489 1259 1503 .94 90 0 -2.175 -2.287 .171 .181 100 100 98 96 5.647 4.517 .177 .164 1.37 .221 .205 .169 6620 7152 328 52 3050 8350 18 27 164 173 -2.175
12 9506 9663 0 4273 156 157 32 9151 8055 7849 8140 8346 0 3577 214 206 71 258 9811 10069 10175 10433 .99 90 0 .101 .098 .899 .863 100 100 100 100 1.166 .933 .858 .856 1.441 1.072 1.07 .849 17000 17646 312 52 3190 8350 18 27 178 187 .101
13 890 1043 0 446 155 153 32 852 1981 1774 1700 1907 0 1046 210 207 72 259 2218 2476 2125 2384 .96 100 0 1.38 1.256 2.046 2.091 98 98 100 100 .48 .384 2.082 1.91 1.535 2.603 2.388 2.225 2626 2590 353 80 3350 8350 18 28 194 204 1.38
14 405 558 0 142 154 153 29 424 1292 1093 1170 1369 0 359 206 199 68 249 1366 1615 1463 1711 .94 110 0 1.688 1.852 2.581 2.688 100 100 100 100 .388 .31 2.578 2.889 1.337 3.222 3.611 2.648 1517 1575 394 80 3480 8350 17 28 206 217 1.688
15 365 519 0 204 154 154 27 400 4777 4580 4377 4574 0 1828 209 197 71 246 5725 5971 5471 5718 .93 100 0 3.839 3.906 12.333 11.822 100 100 100 100 .087 .07 11.45 11.992 1.522 14.313 14.99 11.568 4980 4742 361 80 3640 8350 18 28 223 233 3.839
16 6678 6821 0 2534 156 143 173 7028 14766 14574 14099 14291 0 4493 216 192 338 240 18218 18458 17624 17864 .98 110 0 1.374 1.4 2.143 2.07 100 100 100 100 .482 .386 2.074 2.111 1.266 2.592 2.639 2.029 21602 20777 373 80 3790 8350 17 28 237 248 1.374
17 2158 2299 0 801 151 141 164 1905 16886 16697 18826 19015 0 6155 210 189 320 236 20871 21108 23533 23769 .84 120 0 3.454 3.447 9.272 8.77 97 95 100 100 .114 .091 8.765 8.724 1.361 10.956 10.905 7.02 18602 20984 416 120 3930 8350 17 29 251 263 3.454
18 7 152 0 85 147 145 31 33 209 21 8 196 0 73 195 188 58 235 26 261 10 245 .31 100 -50 .515 1.719 1.778 31 18 27 10 1.571 1.257 .636 1.143 4.021 .795 1.429 1.682 54 15 318 80 4070 8340 17 27 266 276 -.33
19 4020 4173 0 979 778 153 4846 3786 2258 2049 2197 2406 0 606 1433 209 7230 261 2561 2823 2746 3008 .97 90 0 -.564 -.55 .532 .538 9 0 0 0 1.848 1.478 .541 .547 1.264 .677 .683 .534 5835 6217 251 52 4210 8340 17 26 280 289 -.564
20 1657 1809 0 670 1077 152 5989 1526 1848 1634 1739 1953 0 760 1998 214 8818 268 2043 2310 2174 2441 .85 120 0 .421 .392 1.006 1.049 0 0 0 0 .934 .747 1.071 1.049 1.724 1.338 1.312 1.582 3160 3396 444 120 4360 8350 17 29 294 306 .421

Total number of rows: 43008

Table truncated, full table size 9384 Kbytes.




Supplementary data files not provided
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