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Sample GSM6261 Query DataSets for GSM6261
Status Public on Apr 15, 2004
Title AML 62
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 62
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=690650LaserPower=3.544.6
Lot batch = shcz064
 
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 GPL318
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
1 450 594 0 176 147 144 37 428 1426 1309 1218 1335 0 578 120 117 38 131 1471 1602 1369 1500 .85 100 0 1.781 1.605 3.075 3.253 100 97 100 100 .327 .291 3.058 2.707 1.552 3.436 3.041 3.43 1737 1668 410 80 1600 8260 61 71 39 49 1.781
2 3522 3669 0 1775 153 147 51 4123 1648 1531 1412 1529 0 534 129 117 81 131 1720 1852 1587 1718 .97 90 0 -1.261 -1.151 .382 .394 100 100 100 100 2.693 2.397 .371 .401 1.227 .417 .45 .35 5654 4934 312 52 1750 8260 61 70 54 63 -1.261
3 1442 1585 0 965 148 143 42 1773 1816 1697 1491 1610 0 809 123 119 40 134 1907 2040 1675 1809 .96 90 0 .105 .216 .995 .983 100 100 100 100 1.045 .93 .957 1.034 1.3 1.075 1.162 .969 3470 2933 302 52 1890 8260 61 70 68 77 .105
4 549 692 0 220 146 143 38 579 639 519 513 633 0 189 123 120 40 135 583 718 576 711 .9 90 0 .01 .07 .895 .857 100 100 100 100 1.116 .993 .896 .934 1.424 1.007 1.05 .852 1098 1062 313 52 2040 8260 61 70 83 92 .01
5 286 430 0 238 148 144 34 340 275 159 148 264 0 98 120 116 38 130 179 309 166 297 .81 100 0 -.928 -.782 .486 .465 97 92 88 81 2.138 1.903 .468 .517 1.963 .525 .581 .4 499 434 364 80 2190 8260 61 71 98 108 -.928
6 316 462 0 112 152 146 37 330 389 265 251 375 0 86 130 124 42 139 298 437 282 421 .87 70 0 -.148 -.164 .819 .757 100 100 100 100 1.245 1.108 .803 .794 1.431 .902 .892 .789 595 567 206 32 2330 8250 61 68 113 120 -.148
7 327 475 0 243 153 148 39 368 986 869 770 887 0 545 123 117 37 131 976 1108 865 997 .93 90 0 1.408 1.404 2.441 2.44 98 98 100 100 .423 .377 2.361 2.355 1.624 2.653 2.646 2.37 1237 1097 332 52 2490 8250 60 69 128 137 1.408
8 348 493 0 107 150 145 36 346 214 101 87 200 0 65 119 113 40 127 113 240 98 225 .51 80 0 -1.608 -1.832 .266 .332 100 100 80 55 3.426 3.049 .292 .25 2.084 .328 .281 .209 447 435 256 52 2630 8250 61 69 143 151 -1.608
9 174 316 0 98 148 142 36 186 330 207 207 330 0 87 126 123 39 138 233 371 233 371 .73 70 0 .322 .419 1.174 1.165 96 93 100 93 .899 .8 1.113 1.19 1.837 1.25 1.337 1.008 393 381 198 32 2770 8250 61 68 157 164 .322
10 324 468 0 154 146 144 34 338 185 65 57 177 0 64 124 120 40 135 73 208 64 199 .43 100 0 -2.21 -2.339 .197 .227 100 98 62 32 5.2 4.628 .192 .176 2.698 .216 .198 .144 403 381 377 80 2930 8250 60 70 172 182 -2.21
11 525 669 0 171 145 144 36 498 470 350 334 454 0 173 125 120 40 135 393 528 375 510 .87 90 0 -.341 -.484 .632 .681 100 100 98 96 1.423 1.266 .703 .636 1.666 .79 .715 .707 848 859 291 52 3060 8240 59 68 185 194 -.341
12 768 911 0 352 147 143 41 798 938 822 792 908 0 365 122 116 40 130 924 1054 890 1020 .95 90 0 .211 .213 1.033 1.019 100 100 100 100 .971 .864 1.03 1.031 1.31 1.157 1.159 1.028 1620 1560 303 52 3220 8240 59 68 201 210 .211
13 369 510 0 220 144 141 36 382 556 441 459 574 0 193 120 115 36 129 496 625 516 645 .89 80 0 .375 .483 1.166 1.216 100 96 100 98 .866 .771 1.154 1.244 1.579 1.297 1.398 1.021 823 828 264 52 3360 8240 60 68 216 224 .375
14 128 264 0 78 139 136 31 136 397 270 281 408 0 150 128 127 43 143 303 446 316 458 .72 60 0 1.157 1.303 1.799 1.833 96 75 96 84 .504 .448 1.985 2.195 2.05 2.231 2.467 2.326 406 409 164 32 3510 8240 61 67 232 238 1.157
15 223 364 0 3443 142 141 34 847 6371 6257 5295 5409 0 3545 121 114 41 128 7030 7158 5949 6078 .32 100 0 3.053 4.738 22.06 23.872 95 88 100 100 .135 .12 7.387 23.744 2.72 8.3 26.679 4.222 7104 5518 371 80 3650 8240 59 69 244 254 3.053
16 1519 1660 0 751 143 141 35 1621 2936 2821 2790 2905 0 1276 122 115 42 129 3170 3299 3135 3264 .96 100 0 .967 1.045 1.837 1.749 97 97 100 100 .575 .511 1.74 1.837 1.509 1.955 2.064 1.728 4442 4309 350 80 3800 8240 59 69 259 269 .967
17 506 649 0 334 146 143 36 581 5687 5569 4610 4728 0 3460 123 118 41 133 6257 6390 5180 5312 .94 100 0 3.429 3.356 9.752 9.556 100 96 100 100 .104 .093 9.585 9.111 1.521 10.77 10.237 10.306 6150 5116 355 80 3950 8230 58 68 274 284 3.429
18 147 295 0 85 152 148 37 156 275 155 149 269 0 102 123 120 44 135 174 309 167 302 .64 70 0 .159 .188 .886 .935 93 84 87 62 1.006 .896 .994 1.014 2.338 1.116 1.139 1.098 311 296 178 32 4090 8230 59 66 289 296 .159
19 213 358 0 193 151 145 38 258 433 314 223 342 0 285 122 119 43 134 353 487 251 384 .78 100 0 .452 .234 1.12 1.321 91 81 87 77 .822 .731 1.217 1.047 2.253 1.367 1.176 1.453 572 436 370 80 4230 8230 58 68 302 312 .452
20 340 486 0 210 149 146 38 383 498 381 352 469 0 161 122 117 39 131 428 560 396 527 .76 80 0 .161 .218 1.018 1.088 100 98 100 98 1.005 .895 .995 1.035 1.785 1.118 1.163 .893 764 692 254 52 4390 8230 59 67 319 327 .161

Total number of rows: 43008

Table truncated, full table size 9272 Kbytes.




Supplementary data files not provided
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