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Sample GSM6263 Query DataSets for GSM6263
Status Public on Apr 15, 2004
Title AML 78
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 78
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=3.774.62
Lot batch = shcz066
 
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
1 110 242 0 125 180 132 1013 134 782 697 603 688 0 478 87 85 25 123 1010 1133 874 997 .75 100 0 2.914 2.99 5.225 5.188 0 0 100 96 .192 .133 5.201 5.482 2.486 7.538 7.945 5.458 831 713 447 80 1770 8050 52 62 44 54 2.914
2 597 721 0 492 127 124 32 680 453 366 340 427 0 238 88 87 27 126 530 657 493 619 .95 80 0 -.358 -.277 .561 .563 96 94 94 94 1.858 1.282 .538 .57 1.487 .78 .825 .497 1046 937 232 52 1920 8060 54 62 60 68 -.358
3 645 773 0 816 130 128 31 895 323 236 204 291 0 204 92 87 32 126 342 468 296 422 .93 80 0 -1.388 -1.125 .261 .284 92 88 78 69 3.792 2.617 .264 .316 2.301 .382 .458 .242 1131 849 250 52 2060 8060 54 62 74 82 -1.388
4 218 347 0 262 133 129 34 276 1030 941 947 1036 0 546 94 89 33 129 1364 1493 1372 1501 .86 80 0 2.305 2.654 3.935 3.966 90 80 100 100 .293 .202 3.409 4.344 1.839 4.941 6.296 3.067 1217 1165 269 52 2220 8060 54 62 90 98 2.305
5 130 266 0 122 147 136 51 166 182 92 88 178 0 64 95 90 30 130 133 264 128 258 .55 60 0 -.316 -.028 .546 .533 87 71 81 62 1.804 1.245 .554 .677 1.935 .803 .981 .371 258 218 146 32 2340 8050 54 60 103 109 -.316
6 130 266 0 66 142 136 51 152 242 148 137 231 0 61 100 94 30 136 214 351 199 335 .58 50 0 .497 .611 .989 1.019 100 75 100 100 1.027 .709 .974 1.054 1.688 1.411 1.527 .769 300 267 98 12 2500 8050 54 59 119 124 .497
7 191 319 0 227 132 128 37 233 520 433 368 455 0 260 91 87 29 126 628 754 533 659 .85 90 0 1.429 1.481 2.073 2.225 86 76 100 98 .538 .371 1.858 1.927 1.831 2.693 2.792 1.564 666 559 347 52 2650 8060 53 62 132 141 1.429
8 172 301 0 128 137 129 63 207 123 38 34 119 0 38 90 85 28 123 55 178 49 172 .95 60 0 -1.91 -1.803 .232 .197 87 78 56 25 5.447 3.759 .184 .198 3.74 .266 .286 .339 245 206 165 32 2800 8050 54 60 149 155 -1.91
9 63 185 0 388 129 122 62 134 147 61 57 143 0 43 92 86 29 125 88 213 83 207 .28 60 -100 .391 .812 1.013 50 15 71 50 2.197 1.516 .455 .905 3.414 .66 1.311 .058 195 120 170 32 2940 8050 54 60 163 169 -.6
10 135 261 0 110 134 126 60 136 104 15 15 104 0 31 92 89 30 129 22 151 22 151 .3 90 0 -2.645 -2.635 .189 .21 75 55 26 9 9.067 6.256 .11 .111 2.345 .16 .161 .112 151 150 327 52 3100 8060 53 62 177 186 -2.645
11 228 354 0 177 130 126 34 253 126 40 37 123 0 43 90 86 27 125 58 183 54 178 .45 70 0 -2.126 -2.088 .252 .147 84 84 56 37 6.325 4.364 .158 .162 4.716 .229 .235 .126 293 265 208 32 3230 8060 54 61 191 198 -2.126
12 1084 1217 0 738 139 133 48 1144 597 503 446 540 0 257 97 94 31 136 729 865 646 783 .89 60 0 -.65 -.746 .484 .444 96 96 100 96 2.274 1.569 .44 .411 1.542 .637 .596 .368 1647 1530 164 32 3370 8070 56 62 206 212 -.65
13 271 393 0 180 126 122 27 275 359 270 285 374 0 163 92 89 28 129 391 520 413 542 .86 60 0 .509 .608 1.015 1.117 93 90 93 90 1.019 .703 .982 1.052 1.679 1.423 1.524 .897 545 556 144 32 3530 8070 56 62 222 228 .509
14 15 139 0 40 127 124 30 19 104 16 13 101 0 33 92 88 27 128 23 151 19 146 .16 100 -50 .329 .841 .954 36 17 30 11 1.188 .819 .842 .867 3.858 1.22 1.256 .33 35 28 341 80 3670 8060 53 63 234 244 .287
15 55 181 0 68 128 126 32 65 2485 2399 2151 2237 0 1606 90 86 26 125 3477 3601 3117 3242 .69 100 0 5.741 5.825 30.159 30.839 68 43 100 100 .027 .019 36.908 39.109 1.971 53.489 56.68 36.796 2464 2206 346 80 3820 8060 53 63 249 259 5.741
16 1544 1670 0 1295 129 126 35 1584 2073 1983 1867 1957 0 1469 93 90 27 130 2874 3004 2706 2836 .97 100 0 .859 .809 1.618 1.294 95 91 100 100 .799 .551 1.252 1.209 2.025 1.814 1.752 1.2 3567 3411 369 80 3960 8060 53 63 263 273 .859
17 303 430 0 278 130 127 35 357 1831 1738 1537 1630 0 1122 95 93 28 135 2519 2654 2228 2362 .92 100 0 2.819 2.878 5.408 5.08 90 85 100 100 .205 .142 4.868 5.073 1.66 7.056 7.352 4.833 2095 1840 349 80 4110 8060 53 63 278 288 2.819
18 33 160 0 70 134 127 65 52 101 9 9 101 0 29 98 92 52 133 13 146 13 146 .07 100 -50 -1.339 .609 .637 32 13 7 0 5.778 3.987 .173 .273 3.318 .251 .395 .049 61 42 366 80 4260 8060 53 63 293 303 -1.995
19 220 352 0 128 136 132 35 212 179 88 78 169 0 67 94 91 26 132 128 259 113 245 .67 60 0 -.733 -.961 .527 .48 84 81 81 75 2.409 1.662 .415 .355 2.49 .602 .514 .364 300 298 164 32 4410 8060 55 61 310 316 -.733
20 156 285 0 114 136 129 62 154 180 86 86 180 0 65 100 94 29 136 125 261 125 261 .48 60 0 -.305 -.324 .585 .567 78 65 81 62 1.791 1.236 .558 .551 2.66 .809 .799 .223 240 242 152 32 4560 8070 56 62 325 331 -.305

Total number of rows: 43008

Table truncated, full table size 8866 Kbytes.




Supplementary data files not provided
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