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Sample GSM6256 Query DataSets for GSM6256
Status Public on Apr 15, 2004
Title AML 79
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 79
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=660650LaserPower=4.564.66
Lot batch = shcz061
 
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
1 278 418 0 202 143 140 35 311 3380 3239 2848 2989 0 2487 149 141 51 125 2866 2991 2520 2645 .85 110 0 3.204 3.18 9.859 11.054 95 87 100 100 .096 .108 10.415 10.245 2.011 9.217 9.066 12.787 3550 3126 493 80 2180 8350 53 64 32 43 3.204
2 825 963 0 398 139 138 30 842 381 241 210 350 0 169 146 140 47 124 213 337 186 310 .6 80 0 -1.981 -2.15 .263 .232 100 100 90 82 3.494 3.948 .286 .255 2.619 .253 .225 .22 1083 1035 244 52 2330 8350 55 63 49 57 -1.981
3 928 1061 0 625 140 133 43 944 773 631 573 715 0 384 149 142 48 126 558 684 507 633 .94 90 0 -.757 -.872 .706 .678 100 96 100 94 1.496 1.691 .668 .617 1.608 .592 .546 .634 1575 1501 313 52 2470 8350 54 63 62 71 -.757
4 472 609 0 192 144 137 45 473 397 257 213 353 0 149 147 140 48 124 227 351 188 312 .68 80 0 -1.056 -1.324 .504 .51 100 100 98 90 1.84 2.08 .543 .451 2.079 .481 .399 .522 730 685 264 52 2620 8350 55 63 78 86 -1.056
5 148 287 0 128 140 139 36 178 315 180 135 270 0 176 144 135 45 119 159 279 119 239 .77 100 0 -.16 -.309 .871 .922 96 77 82 68 .989 1.117 1.011 .912 2.345 .895 .807 1.226 358 283 360 80 2770 8350 54 64 92 102 -.16
6 200 343 0 131 150 143 69 210 424 286 255 393 0 180 149 138 52 122 253 375 226 348 .82 80 0 .269 .174 1.411 1.446 84 71 92 88 .734 .83 1.362 1.275 1.677 1.205 1.128 1.394 496 455 254 52 2920 8350 55 63 108 116 .269
7 302 442 0 138 146 140 43 290 637 490 464 611 0 186 152 147 48 130 434 564 411 541 .84 80 0 .58 .443 1.862 1.734 96 96 100 100 .592 .669 1.69 1.536 1.778 1.495 1.36 1.743 780 766 246 52 3060 8340 54 62 122 130 .58
8 288 439 0 132 161 151 52 298 474 315 324 483 0 173 164 159 54 141 279 419 287 427 .83 90 0 -.096 -.006 .98 1.04 100 98 100 84 .946 1.069 1.057 1.125 1.671 .935 .996 1.164 613 612 335 52 3200 8350 54 63 135 144 -.096
9 134 269 0 85 139 135 33 151 417 278 221 360 0 197 147 139 46 123 246 369 196 319 .79 90 0 .704 .545 1.724 1.714 92 84 96 94 .543 .614 1.841 1.649 1.963 1.629 1.46 2.207 429 355 313 52 3350 8350 54 63 150 159 .704
10 222 358 0 123 139 136 34 240 310 169 59 200 0 233 148 141 46 125 150 274 52 177 .55 100 0 -.682 -2.088 .632 .791 98 96 58 45 1.42 1.605 .704 .266 3.113 .623 .235 1.317 409 281 384 80 3500 8340 53 63 165 175 -.682
11 353 484 0 206 136 131 37 394 366 231 191 326 0 196 141 135 45 119 204 324 169 288 .57 80 0 -.947 -1.062 .469 .484 100 96 80 67 1.706 1.927 .586 .541 3.191 .519 .479 .587 625 544 244 52 3650 8350 55 63 181 189 -.947
12 641 778 0 472 143 137 40 823 1070 931 854 993 0 420 151 139 58 123 824 947 756 879 .94 80 0 .002 .238 1.184 1.123 100 100 100 100 .884 .999 1.131 1.332 1.418 1.001 1.179 1.061 1754 1495 264 52 3790 8350 55 63 195 203 .002
13 306 442 0 182 144 136 47 308 604 464 486 626 0 211 148 140 55 124 411 535 430 554 .86 80 0 .415 .491 1.747 1.671 96 84 100 98 .664 .75 1.506 1.588 1.824 1.333 1.406 1.433 772 792 266 52 3940 8350 55 63 210 218 .415
14 208 341 0 106 142 133 48 241 566 421 396 541 0 275 158 145 72 128 373 501 350 479 .83 70 0 .628 .753 1.495 1.642 96 93 93 81 .572 .647 1.747 1.904 1.791 1.546 1.685 2.167 662 604 203 32 4080 8350 55 62 224 231 .628
15 147 283 0 176 152 136 104 193 3599 3456 2282 2425 0 3130 154 143 63 127 3058 3185 2019 2146 .77 120 0 3.986 3.78 14.156 18.088 56 45 95 92 .056 .063 17.907 15.524 2.619 15.847 13.738 22.781 3649 2429 511 120 4230 8340 52 64 237 249 3.986
16 1677 1815 0 1377 147 138 54 1763 3201 3058 3061 3204 0 2161 157 143 75 127 2706 2833 2709 2835 .97 100 0 .618 .692 1.965 1.836 100 98 100 100 .577 .651 1.735 1.825 1.543 1.535 1.615 1.681 4821 4738 328 80 4370 8340 53 63 252 262 .618
17 314 452 0 472 143 138 45 446 3123 2982 1743 1884 0 2999 154 141 68 125 2639 2764 1542 1667 .95 120 0 2.565 2.296 6.915 6.512 81 72 99 97 .15 .169 6.686 5.551 1.905 5.917 4.912 6.754 3428 2057 461 120 4520 8340 52 64 266 278 2.565
18 261 396 0 125 140 135 36 244 461 325 254 390 0 257 139 136 40 120 288 408 225 345 .73 80 0 .237 -.216 1.114 1.328 94 90 90 82 .751 .848 1.332 .973 2.421 1.179 .861 1.806 569 515 216 52 4670 8340 54 62 283 291 .237
19 292 436 0 152 149 144 43 330 543 404 367 506 0 250 145 139 45 123 358 481 325 448 .79 90 0 .116 .153 1.06 1.158 100 100 96 96 .817 .923 1.224 1.257 2.217 1.083 1.112 1.524 734 659 300 52 4810 8340 53 62 296 305 .116
20 284 429 0 185 151 145 40 329 578 418 390 550 0 289 171 160 75 142 370 512 345 487 .88 90 0 .169 .281 1.119 1.16 100 96 92 78 .787 .889 1.271 1.373 1.779 1.124 1.215 1.451 747 674 306 52 4950 8340 53 62 310 319 .169

Total number of rows: 43008

Table truncated, full table size 9359 Kbytes.




Supplementary data files not provided
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