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Sample GSM6270 Query DataSets for GSM6270
Status Public on Apr 15, 2004
Title AML 76
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 76
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=640650LaserPower=4.024.64
Lot batch = shcz079
 
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
1 267 417 0 168 151 150 31 284 479 344 329 464 0 177 137 135 36 142 362 504 346 488 .83 90 0 .351 .375 1.215 1.179 94 94 100 100 .826 .784 1.211 1.232 1.737 1.275 1.297 1.188 628 596 342 52 1830 7920 31 40 26 35 .351
2 3494 3641 0 2286 155 147 52 3293 7178 7048 7123 7253 0 4397 137 130 43 137 7419 7556 7498 7635 .99 90 0 1.172 1.102 2.462 2.184 100 98 100 100 .467 .444 2.14 2.039 1.426 2.253 2.146 2.074 10341 10617 301 52 1970 7910 30 39 40 49 1.172
3 2342 2500 0 915 380 158 901 2337 1330 1185 1189 1334 0 432 332 145 771 153 1247 1400 1252 1404 .96 70 0 -.906 -.904 .52 .505 90 75 84 15 1.972 1.874 .507 .508 1.308 .534 .534 .514 3522 3531 199 32 2110 7910 31 38 55 62 -.906
4 527 680 0 195 218 153 489 511 410 275 271 406 0 125 194 135 414 142 289 432 285 427 .88 80 0 -.82 -.886 .523 .539 55 0 11 0 1.858 1.765 .538 .514 1.522 .566 .541 .511 786 798 287 52 2260 7920 32 40 70 78 -.82
5 353 506 0 213 158 153 41 324 383 249 240 374 0 137 136 134 34 141 262 403 253 394 .85 90 0 -.306 -.483 .827 .756 86 82 96 94 1.301 1.236 .769 .68 2.025 .809 .716 .677 573 593 290 52 2410 7920 31 40 84 93 -.306
6 372 535 0 158 164 163 36 371 280 142 137 275 0 67 143 138 34 145 149 295 144 289 .64 70 0 -1.312 -1.367 .366 .341 96 96 100 81 2.613 2.482 .383 .368 1.826 .403 .388 .266 513 509 214 32 2550 7920 32 39 99 106 -1.312
7 473 629 0 351 158 156 34 523 880 744 708 844 0 433 140 136 37 143 783 926 745 888 .96 80 0 .582 .656 1.606 1.394 96 92 100 100 .703 .668 1.423 1.497 1.807 1.497 1.576 1.357 1267 1181 275 52 2700 7920 32 40 114 122 .582
8 415 573 0 166 159 158 35 372 271 138 141 274 0 65 138 133 41 140 145 285 148 288 .62 70 0 -1.357 -1.483 .361 .341 93 93 90 78 2.696 2.561 .371 .34 2.603 .39 .358 .279 510 556 223 32 2850 7910 31 38 129 136 -1.357
9 91 250 0 66 158 159 32 100 354 214 226 366 0 62 141 140 35 147 225 373 238 385 .61 60 0 1.172 1.386 2.267 2.246 87 68 100 96 .467 .444 2.14 2.484 1.855 2.253 2.614 1.977 314 317 171 32 2990 7920 33 39 144 150 1.172
10 290 449 0 150 162 159 37 260 191 52 56 195 0 38 143 139 34 146 55 201 59 205 .29 90 0 -2.248 -2.299 .204 .195 88 84 67 38 5 4.75 .2 .193 3.278 .211 .203 .098 312 346 329 52 3140 7930 32 41 157 166 -2.248
11 913 1071 0 198 186 158 108 883 266 114 102 254 0 64 154 152 40 160 120 280 107 267 .74 50 0 -2.879 -3.088 .113 .117 100 100 100 58 7.746 7.358 .129 .112 1.868 .136 .118 .124 997 1015 104 12 3280 7910 32 37 173 178 -2.879
12 1454 1619 0 987 172 165 48 1595 1401 1259 1093 1235 0 671 152 142 53 149 1325 1475 1151 1300 .97 70 0 -.267 -.338 .857 .841 100 100 100 100 1.267 1.204 .789 .752 1.37 .831 .791 .736 2854 2547 236 32 3440 7910 31 38 188 195 -.267
13 588 743 0 314 165 155 72 634 484 347 346 483 0 146 147 137 50 144 365 509 364 508 .89 70 0 -.796 -.691 .57 .555 100 100 100 96 1.827 1.736 .547 .588 1.537 .576 .619 .474 981 934 228 32 3590 7910 31 38 203 210 -.796
14 41 201 0 52 164 160 39 51 224 85 74 213 0 62 143 139 35 146 89 236 78 224 .14 60 0 .811 .926 1.91 1.853 50 31 81 53 .6 .57 1.667 1.805 3.814 1.754 1.9 1.22 136 115 150 32 3730 7920 33 39 218 224 .811
15 600 762 0 376 164 162 36 601 1334 1194 1236 1376 0 564 142 140 37 147 1257 1404 1301 1448 .95 80 0 1.064 1.117 2.369 2.04 96 96 100 100 .503 .478 1.987 2.06 1.715 2.091 2.168 1.876 1795 1836 280 52 3870 7920 32 40 231 239 1.064
16 3918 4081 0 2403 168 163 45 3562 5796 5660 6318 6454 0 3324 150 136 68 143 5958 6101 6651 6794 .98 90 0 .742 .763 2.138 1.591 98 98 100 100 .629 .598 1.589 1.613 1.972 1.673 1.697 1.503 9222 10236 289 52 4020 7910 30 39 245 254 .742
17 572 736 0 457 168 164 43 628 6109 5970 5681 5820 0 3847 145 139 55 146 6284 6431 5980 6126 .95 100 0 3.323 3.386 10.287 9.894 93 91 100 100 .105 .1 9.506 9.932 1.657 10.007 10.455 9.474 6598 6253 376 80 4170 7920 31 41 260 270 3.323
18 121 284 0 69 162 163 35 125 197 63 64 198 0 43 138 134 36 141 66 207 67 208 .24 60 0 -.915 -.845 .505 .474 90 84 75 40 1.984 1.885 .504 .529 2.216 .531 .557 .198 188 185 165 32 4320 7910 32 38 277 283 -.915
19 230 390 0 206 163 160 35 245 290 146 134 278 0 100 148 144 39 152 154 305 141 293 .79 80 0 -.673 -.705 .633 .595 82 76 80 75 1.678 1.594 .596 .583 1.799 .627 .613 .506 391 364 277 52 4470 7920 32 40 291 299 -.673
20 321 484 0 175 164 163 33 308 415 270 245 390 0 134 146 145 34 153 284 437 258 411 .86 70 0 -.116 -.316 .927 .824 90 90 93 93 1.141 1.084 .877 .763 2.254 .923 .803 .811 578 566 192 32 4610 7920 32 39 305 312 -.116

Total number of rows: 43008

Table truncated, full table size 9161 Kbytes.




Supplementary data files not provided
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