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Sample GSM6333 Query DataSets for GSM6333
Status Public on Apr 15, 2004
Title AML 71
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 71
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=650650LaserPower=4.664.64
Lot batch = shdj100
 
Submission date May 07, 2003
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
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 �m 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 �m 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 �m 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
1 495 637 0 286 142 142 30 485 1751 1634 1676 1793 0 771 119 117 32 123 1720 1843 1764 1887 .95 90 0 1.826 1.834 3.387 3.213 90 88 100 100 .297 .282 3.369 3.386 1.439 3.546 3.564 3.309 2119 2171 332 52 1540 8110 26 35 17 26 1.826
2 5823 5966 0 2680 145 143 34 5554 2309 2192 2052 2169 0 1092 121 117 40 123 2307 2431 2160 2283 .98 90 0 -1.267 -1.431 .419 .406 100 100 100 100 2.534 2.407 .395 .352 1.504 .415 .371 .384 7746 7875 336 52 1690 8100 25 34 32 41 -1.267
3 858 1000 0 1356 144 142 38 1375 1115 1004 640 751 0 915 120 111 40 117 1057 1174 674 791 .98 60 0 -.38 -.349 .91 .733 96 96 100 100 1.37 1.301 .73 .746 2.076 .769 .785 .691 2379 1498 166 32 1840 8100 27 33 49 55 -.38
4 576 717 0 507 142 141 32 644 496 383 376 489 0 256 114 113 29 119 403 522 396 515 .92 80 0 -.676 -.541 .648 .597 90 84 96 92 1.681 1.597 .595 .653 1.668 .626 .687 .531 1027 952 233 52 1980 8110 27 35 62 70 -.676
5 1866 2009 0 959 144 143 33 1813 2058 1945 1956 2069 0 1081 116 113 31 119 2047 2166 2059 2178 .97 80 0 .175 .142 1.117 1.075 96 96 100 98 .932 .886 1.073 1.048 1.702 1.129 1.103 1.083 3758 3822 254 52 2120 8100 26 34 76 84 .175
6 867 1011 0 746 147 144 34 954 1545 1424 1218 1339 0 1000 123 121 32 127 1499 1626 1282 1409 .98 80 0 .652 .564 1.668 1.49 96 94 98 98 .67 .636 1.493 1.405 1.537 1.571 1.479 1.434 2378 2085 242 52 2270 8110 27 35 91 99 .652
7 1607 1753 0 1257 148 146 36 1663 4769 4654 4343 4458 0 3083 117 115 32 121 4899 5020 4572 4693 .97 90 0 1.559 1.508 3.499 2.899 96 92 100 100 .357 .339 2.799 2.703 1.981 2.946 2.845 2.728 6317 5950 302 52 2410 8110 26 35 104 113 1.559
8 1181 1328 0 490 151 147 33 1172 385 270 258 373 0 137 118 115 32 121 284 405 272 393 .93 70 0 -2.044 -2.121 .223 .217 100 100 100 100 4.341 4.124 .23 .218 1.313 .243 .23 .23 1442 1439 207 32 2560 8100 26 33 120 127 -2.044
9 599 737 0 341 141 138 34 587 1216 1110 1193 1299 0 550 111 106 33 112 1168 1280 1256 1367 .96 100 0 .993 1.068 2.1 1.911 93 90 100 100 .529 .502 1.891 1.992 1.625 1.99 2.096 1.83 1697 1792 398 80 2710 8100 25 35 134 144 .993
10 576 720 0 184 145 144 39 538 299 195 206 310 0 83 111 104 32 109 205 315 217 326 .89 60 0 -1.39 -1.409 .344 .37 100 100 100 93 2.759 2.621 .362 .358 1.546 .382 .376 .349 733 782 152 32 2850 8100 27 33 150 156 -1.39
11 7296 7440 0 2676 146 144 31 6889 929 815 772 886 0 396 117 114 33 120 858 978 813 933 .95 90 0 -3.005 -3.166 .113 .122 100 100 100 100 8.453 8.03 .118 .106 1.429 .125 .111 .113 7704 8068 317 52 2990 8100 25 34 162 171 -3.005
12 7190 7334 0 6215 146 144 32 7976 11491 11377 10463 10577 0 7939 118 114 34 120 11976 12096 11014 11134 .99 100 0 .586 .615 1.933 1.46 100 96 100 100 .701 .666 1.426 1.455 2.051 1.501 1.532 1.361 19353 17653 355 80 3150 8110 26 36 178 188 .586
13 1881 2023 0 572 147 142 36 1677 1435 1324 1382 1493 0 515 116 111 40 117 1394 1511 1455 1572 .97 90 0 -.267 -.371 .774 .772 100 100 100 100 1.267 1.203 .79 .735 1.301 .831 .773 .798 3001 3263 273 52 3290 8090 24 33 192 201 -.267
14 546 694 0 300 153 148 38 582 501 398 368 471 0 205 107 103 36 108 419 527 387 496 .94 120 0 -.474 -.495 .687 .679 99 98 97 96 1.462 1.389 .684 .674 1.403 .72 .709 .67 980 914 437 120 3440 8100 24 36 206 218 -.474
15 1443 1593 0 712 155 150 37 1412 660 556 591 695 0 279 104 104 28 109 585 695 622 732 .97 100 0 -1.271 -1.214 .383 .392 100 100 100 97 2.54 2.413 .394 .41 1.504 .414 .431 .383 1968 2034 305 80 3580 8100 25 35 221 231 -1.271
16 7542 7685 0 3680 144 143 30 7969 19038 18932 17838 17944 0 8029 120 106 81 112 19928 20040 18777 18888 .99 110 0 1.322 1.316 2.468 2.394 100 100 100 100 .421 .4 2.376 2.365 1.284 2.501 2.49 2.341 26901 25380 386 80 3730 8100 24 35 235 246 1.322
17 2157 2297 0 709 142 140 32 1927 52339 52229 60358 60468 28 15783 122 110 78 116 54978 55094 63535 63651 .99 120 0 4.834 4.88 28.148 26.759 100 100 100 100 .037 .035 27.104 27.982 1.229 28.53 29.455 26.444 54156 62515 426 120 3880 8100 24 36 250 262 4.834
18 37 174 0 79 141 137 31 45 156 48 37 145 0 62 111 108 31 114 51 164 39 153 .51 100 -50 .074 1.113 1.107 55 18 55 31 .938 .891 1.067 1 2.357 1.123 1.053 .789 93 74 316 80 4020 8090 24 34 265 275 .167
19 4734 4874 0 1980 145 140 32 4060 3004 2898 3149 3255 0 1191 110 106 30 112 3051 3162 3315 3426 .98 100 0 -.412 -.514 .798 .714 100 100 100 100 1.401 1.331 .714 .665 1.547 .751 .7 .676 6958 7883 306 80 4170 8100 25 35 280 290 -.412
20 2299 2442 0 772 144 143 33 2066 1545 1441 1542 1646 0 526 109 104 31 109 1517 1626 1623 1733 .98 120 0 -.446 -.502 .713 .707 100 100 100 100 1.434 1.362 .697 .671 1.276 .734 .706 .685 3507 3841 413 120 4320 8100 24 36 294 306 -.446

Total number of rows: 43008

Table truncated, full table size 9502 Kbytes.




Supplementary data files not provided
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