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Sample GSM6339 Query DataSets for GSM6339
Status Public on Apr 15, 2004
Title AML 31
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 31
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=4.513.86
Lot batch = shdj106
 
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
1 310 434 0 217 126 124 28 326 5527 5422 5537 5642 0 2543 112 105 35 114 5893 6008 6018 6133 .91 80 0 4.176 4.279 18.695 16.67 92 88 100 100 .06 .055 16.632 17.861 1.723 18.078 19.414 16.231 5748 5847 268 52 1480 8590 19 27 16 24 4.176
2 3279 3401 0 1172 173 122 292 2851 1254 1136 1224 1342 0 448 146 118 145 128 1235 1363 1330 1459 .96 70 0 -1.207 -1.301 .396 .403 100 100 96 96 2.51 2.309 .398 .373 1.378 .433 .406 .387 3987 4503 211 32 1610 8580 18 25 29 36 -1.207
3 577 701 0 1070 126 124 29 991 909 796 530 643 0 749 114 113 36 123 865 988 576 699 .95 70 0 -.196 -.002 1.101 .865 90 84 100 96 1.245 1.145 .803 .919 2.179 .873 .998 .729 1787 1107 218 32 1770 8590 19 26 45 52 -.196
4 398 523 0 375 127 125 30 488 425 318 265 372 0 206 109 107 32 116 346 462 288 404 .84 80 0 -.498 -.466 .771 .686 96 84 98 92 1.535 1.412 .652 .666 2.721 .708 .724 .544 806 663 240 52 1920 8590 19 27 60 68 -.498
5 964 1083 0 804 125 119 32 1029 4609 4505 4246 4350 0 3268 111 104 37 113 4897 5010 4615 4728 .96 80 0 2.251 2.259 4.944 4.725 96 92 100 100 .228 .21 4.378 4.405 1.707 4.759 4.788 4.402 5534 5210 264 52 2060 8580 18 26 74 82 2.251
6 929 1049 0 423 125 120 35 968 2003 1890 1728 1841 0 863 118 113 37 123 2054 2177 1878 2001 .95 70 0 1.086 1.016 1.937 1.912 100 100 100 100 .512 .471 1.952 1.86 1.425 2.122 2.022 2.017 2858 2657 219 32 2210 8580 18 25 89 96 1.086
7 887 1014 0 1024 128 127 28 1186 4604 4496 3399 3507 0 3529 113 108 33 117 4887 5004 3695 3812 .95 80 0 2.043 2.058 4.406 3.647 96 88 100 100 .264 .243 3.791 3.832 2.108 4.121 4.165 3.757 5682 4286 269 52 2360 8590 19 27 104 112 2.043
8 617 744 0 281 130 127 30 572 445 335 381 491 0 166 112 110 31 120 364 484 414 534 .9 70 0 -.652 -.575 .619 .565 96 96 100 96 1.707 1.571 .586 .618 2.347 .637 .671 .57 907 998 198 32 2490 8580 18 25 117 124 -.652
9 467 588 0 197 124 121 28 457 337 229 208 316 0 140 112 108 34 117 249 366 226 343 .84 80 0 -.877 -1.047 .481 .479 98 96 96 88 1.996 1.836 .501 .445 1.742 .545 .484 .505 686 675 284 52 2640 8580 18 26 132 140 -.877
10 400 523 0 166 124 123 27 402 290 181 185 294 0 90 113 109 37 118 197 315 201 320 .8 70 0 -1.031 -.992 .422 .466 100 100 93 90 2.221 2.043 .45 .463 1.665 .489 .503 .413 583 585 206 32 2790 8580 18 25 147 154 -1.031
11 3774 3896 0 1613 125 122 30 3643 817 709 703 811 0 356 112 108 33 117 771 888 764 882 .92 90 0 -2.241 -2.304 .198 .208 98 96 98 98 5.138 4.727 .195 .186 1.952 .212 .202 .179 4352 4477 328 52 2930 8580 17 26 160 169 -2.241
12 6324 6445 0 3495 125 121 32 6614 12604 12493 12702 12813 0 5953 116 111 36 121 13579 13700 13807 13927 .97 90 0 1.038 1.126 1.984 1.94 100 100 100 100 .529 .487 1.889 2.009 1.37 2.053 2.183 1.858 19107 19026 312 52 3080 8580 17 26 175 184 1.038
13 1031 1160 0 459 133 129 37 971 5433 5321 5244 5356 0 2830 119 112 51 122 5784 5905 5700 5822 .92 90 0 2.574 2.467 5.58 5.749 98 96 100 100 .182 .168 5.48 5.086 1.745 5.956 5.529 5.724 6292 6275 288 52 3220 8580 17 26 189 198 2.574
14 439 568 0 190 136 129 40 459 422 310 321 433 0 126 122 112 54 122 337 459 349 471 .85 100 0 -.446 -.331 .646 .688 98 97 96 93 1.481 1.362 .675 .731 1.62 .734 .795 .623 769 760 382 80 3360 8580 17 27 203 213 -.446
15 713 843 0 297 135 130 39 685 21687 21574 23204 23317 0 7901 177 113 364 123 23450 23573 25222 25345 .95 90 0 5.097 5.145 31.084 31.024 96 94 100 100 .032 .029 31.495 32.544 1.278 34.234 35.374 32.562 22259 23917 311 52 3510 8580 17 26 218 227 5.097
16 4808 4936 0 3027 135 128 56 5352 8295 8175 8010 8130 0 3428 169 120 320 130 8886 9016 8707 8837 .96 110 0 .731 .857 1.798 1.474 100 98 100 100 .655 .602 1.527 1.666 2.137 1.66 1.811 1.425 13527 12818 425 80 3680 8590 17 28 234 245 .731
17 1728 1853 0 449 130 125 32 1632 25419 25302 27367 27484 0 6535 171 117 366 127 27502 27629 29747 29874 .95 110 0 4.075 4.106 15.63 15.879 100 100 100 100 .065 .059 15.504 15.837 1.183 16.852 17.215 16.462 26934 29095 369 80 3810 8580 16 27 247 258 4.075
18 17 141 0 294 127 124 32 93 217 102 17 132 0 276 168 115 364 125 111 236 18 143 .33 100 -50 .12 1.462 1.513 32 22 8 2 .912 .839 1.097 1 3.38 1.192 1.087 6.733 195 34 363 80 3960 8570 16 26 263 273 .254
19 3188 3308 0 654 124 120 29 3085 1859 1746 1756 1869 0 313 118 113 38 123 1898 2021 1909 2032 .97 90 0 -.701 -.74 .586 .571 100 100 100 100 1.767 1.626 .566 .551 1.391 .615 .599 .545 4831 4944 264 52 4100 8580 17 26 277 286 -.701
20 1485 1612 0 502 130 127 30 1426 626 515 544 655 0 221 115 111 35 121 560 680 591 712 .91 110 0 -1.349 -1.328 .348 .358 100 100 98 96 2.769 2.547 .361 .366 1.516 .393 .398 .358 1941 2029 402 80 4250 8580 16 27 291 302 -1.349

Total number of rows: 43008

Table truncated, full table size 9467 Kbytes.




Supplementary data files not provided
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