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Sample GSM6287 Query DataSets for GSM6287
Status Public on Apr 15, 2004
Title AML 60
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 60
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=670650LaserPower=3.965.37
Lot batch = shcz112
 
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 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 �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 85 130 0 71 55 45 28 99 218 163 129 184 0 115 63 55 31 62 183 245 145 207 .74 70 0 .887 .77 1.697 1.756 87 65 93 81 .607 .541 1.646 1.518 2.087 1.85 1.705 1.883 262 214 194 32 1510 8200 52 59 27 34 .887
2 277 324 0 366 55 47 27 447 678 617 407 468 0 435 67 61 29 69 693 762 457 526 .96 70 0 .633 .723 1.604 1.434 100 93 100 100 .724 .645 1.38 1.469 1.489 1.551 1.651 1.28 1064 684 214 32 1670 8190 51 58 43 50 .633
3 266 313 0 217 51 47 19 308 393 333 245 305 0 242 62 60 24 67 374 442 275 343 .94 70 0 .281 .049 1.049 1.08 100 100 100 100 .925 .823 1.081 .921 1.597 1.215 1.035 1.114 641 511 216 32 1800 8190 51 58 56 63 .281
4 92 138 0 71 51 46 20 108 118 62 55 111 0 47 60 56 23 63 70 133 62 125 .71 70 0 -.633 -.574 .622 .612 93 81 75 56 1.742 1.55 .574 .598 2.011 .645 .672 .62 170 147 224 32 1940 8200 52 59 70 77 -.633
5 97 142 0 65 49 45 19 104 161 104 77 134 0 85 59 57 23 64 117 181 87 151 .81 80 0 .168 -.165 .949 1 94 86 84 67 1 .89 1 .794 2.027 1.124 .892 1.167 208 174 286 52 2090 8190 51 59 85 93 .168
6 120 168 0 56 52 48 15 125 120 65 63 118 0 47 59 55 22 62 73 135 71 133 .59 50 0 -.775 -.761 .521 .595 100 100 75 58 1.923 1.712 .52 .525 1.624 .584 .59 .481 190 183 98 12 2240 8190 52 57 101 106 -.775
7 148 194 0 113 49 46 15 171 422 366 281 337 0 231 59 56 22 63 411 474 316 379 .92 70 0 1.266 1.093 2.163 2.134 100 96 100 96 .467 .416 2.14 1.899 1.596 2.405 2.133 2.171 537 429 226 32 2390 8190 51 58 115 122 1.266
8 151 202 0 66 57 51 26 169 129 65 70 134 0 40 69 64 28 72 73 145 79 151 .68 50 0 -1.21 -.941 .398 .414 100 100 83 66 2.6 2.314 .385 .464 1.901 .432 .521 .414 234 221 98 12 2520 8190 52 57 129 134 -1.21
9 96 139 0 40 47 43 16 102 279 219 209 269 0 105 65 60 24 67 246 313 235 302 .85 70 0 1.27 1.291 2.044 2.046 100 100 100 100 .466 .415 2.147 2.177 1.585 2.412 2.446 2.484 321 305 212 32 2680 8200 52 59 144 151 1.27
10 73 115 0 54 46 42 15 87 85 29 19 75 0 40 59 56 23 63 33 96 21 84 .55 80 0 -1.417 -1.774 .322 .378 100 88 44 23 3 2.67 .333 .26 2.607 .375 .292 .506 116 92 289 52 2820 8190 51 59 158 166 -1.417
11 359 403 0 202 47 44 15 390 169 115 119 173 0 52 57 54 22 61 129 190 134 194 .86 60 0 -1.594 -1.425 .291 .35 100 100 96 87 3.391 3.018 .295 .331 1.818 .331 .372 .259 505 478 170 32 2970 8190 52 58 174 180 -1.594
12 193 235 0 300 46 42 15 301 599 548 323 374 0 520 55 51 18 57 616 673 363 420 .96 60 0 1.033 .911 1.788 1.812 96 90 100 93 .549 .489 1.821 1.674 1.595 2.046 1.88 1.805 849 516 170 32 3120 8190 52 58 189 195 1.033
13 135 180 0 90 49 45 19 133 198 149 152 201 0 96 53 49 17 55 167 222 171 226 .84 60 0 .332 .339 1.126 1.208 90 84 93 87 .893 .794 1.12 1.126 1.845 1.259 1.265 1.126 282 287 164 32 3280 8200 53 59 205 211 .332
14 49 91 0 35 45 42 15 50 79 31 27 75 0 27 51 48 17 54 35 89 30 84 .44 60 0 -.522 -.692 .599 .55 84 62 68 37 1.613 1.435 .62 .551 3.134 .697 .619 .626 81 76 155 32 3420 8180 51 57 219 225 -.522
15 143 185 0 90 44 42 13 160 351 301 266 316 0 163 60 50 91 56 338 394 299 355 .9 80 0 1.08 1.064 1.943 1.837 98 98 96 71 .532 .473 1.881 1.86 1.744 2.114 2.09 1.972 461 409 280 52 3560 8190 51 59 232 240 1.08
16 441 483 0 354 44 42 11 536 1128 1079 888 937 0 623 54 49 20 55 1212 1267 998 1053 .98 80 0 1.178 1.178 2.199 2.084 100 100 100 100 .497 .442 2.013 2.014 1.41 2.262 2.262 1.943 1615 1329 277 52 3710 8190 51 59 247 255 1.178
17 160 202 0 100 44 42 12 167 998 946 819 871 0 522 56 52 20 58 1063 1121 920 979 .93 80 0 2.67 2.524 5.994 6.182 98 94 100 100 .177 .157 5.665 5.119 1.462 6.365 5.751 5.769 1113 979 286 52 3860 8190 51 59 262 270 2.67
18 107 151 0 22 47 44 14 111 79 23 25 81 0 24 57 56 19 63 26 89 28 91 .5 50 0 -2.103 -1.929 .256 .294 100 100 58 25 4.826 4.295 .207 .234 2.584 .233 .263 .374 134 132 98 12 4000 8180 51 56 277 282 -2.103
19 196 238 0 154 44 42 13 221 216 167 145 194 0 129 53 49 19 55 188 243 163 218 .93 60 0 -.236 -.267 .685 .685 100 96 87 84 1.323 1.178 .756 .74 1.606 .849 .831 .783 388 341 164 32 4140 8200 53 59 291 297 -.236
20 172 211 0 139 41 39 10 201 263 216 207 254 0 147 50 47 17 53 243 296 233 285 .92 60 0 .272 .435 1.071 1.154 100 100 100 90 .931 .828 1.075 1.203 1.683 1.207 1.352 1.069 417 379 160 32 4290 8170 50 56 306 312 .272

Total number of rows: 43008

Table truncated, full table size 8775 Kbytes.




Supplementary data files not provided
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