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Sample GSM6265 Query DataSets for GSM6265
Status Public on Apr 15, 2004
Title AML 43
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 43
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=700650LaserPower=3.64.71
Lot batch = shcz074
 
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
1 222 368 0 101 150 146 35 220 627 490 415 552 0 229 138 137 42 199 710 909 601 800 .83 90 0 1.691 1.438 2.261 2.267 100 94 100 100 .449 .31 2.227 1.869 1.621 3.228 2.709 2.538 710 637 345 52 1840 7740 45 54 27 36 1.691
2 4030 4169 0 1833 144 139 36 3732 241 119 120 242 0 86 129 122 45 177 172 349 174 351 .68 80 0 -4.436 -4.534 .039 .037 100 100 78 65 31.361 21.639 .032 .03 2.241 .046 .043 .027 3851 4150 266 52 1990 7740 46 54 43 51 -4.436
3 1241 1383 0 555 156 142 60 1387 677 544 521 654 0 259 134 133 42 193 788 981 755 948 .94 70 0 -.815 -.717 .378 .376 100 100 100 100 2.55 1.759 .392 .42 1.304 .568 .608 .407 1931 1762 198 32 2130 7740 46 53 57 64 -.815
4 427 566 0 251 146 139 43 475 195 68 73 200 0 68 130 127 42 184 99 283 106 290 .52 80 0 -2.269 -2.013 .165 .178 98 96 63 42 6.985 4.82 .143 .171 2.955 .207 .248 .126 543 500 276 52 2280 7740 46 54 72 80 -2.269
5 262 411 0 111 151 149 34 275 301 168 162 295 0 80 136 133 43 193 243 436 235 428 .71 90 0 -.176 -.158 .588 .592 100 100 98 84 1.637 1.129 .611 .618 1.836 .885 .896 .545 443 424 314 52 2420 7740 45 54 85 94 -.176
6 219 371 0 119 151 152 33 230 234 105 105 234 0 53 134 129 42 187 152 339 152 339 .53 70 0 -.596 -.525 .509 .467 96 90 90 62 2.19 1.511 .457 .479 2.645 .662 .695 .409 335 324 220 32 2570 7730 45 52 101 108 -.596
7 394 528 0 225 139 134 30 431 698 570 605 733 0 261 128 128 37 186 826 1012 877 1062 .92 80 0 .939 1.154 1.4 1.355 98 98 100 100 .756 .522 1.323 1.536 1.631 1.917 2.225 1.297 1001 999 275 52 2720 7740 46 54 116 124 .939
8 222 360 0 134 139 138 30 244 203 76 79 206 0 57 129 127 39 184 110 294 114 299 .36 80 0 -1.147 -.955 .354 .368 100 90 73 50 3.211 2.215 .311 .356 2.893 .451 .516 .185 320 301 233 52 2860 7740 46 54 130 138 -1.147
9 106 245 0 61 142 139 32 108 194 69 64 189 0 58 131 125 41 181 100 281 93 274 .36 80 0 -.111 -.193 .65 .755 88 75 61 36 1.565 1.08 .639 .604 2.52 .926 .875 .604 177 170 255 52 3000 7740 46 54 144 152 -.111
10 266 405 0 90 142 139 34 265 171 45 47 173 0 60 130 126 42 183 65 248 68 251 .24 90 0 -2.023 -1.965 .231 .269 100 96 50 26 5.889 4.063 .17 .177 3.201 .246 .256 .116 310 313 337 52 3150 7740 45 54 158 167 -2.023
11 434 579 0 208 153 145 48 406 196 68 75 203 0 69 133 128 41 186 99 284 109 294 .21 60 0 -2.043 -1.997 .242 .19 100 96 62 46 5.971 4.12 .167 .173 2.892 .243 .25 .072 474 509 165 32 3300 7730 46 52 175 181 -2.043
12 606 754 0 530 153 148 41 701 700 574 475 601 0 394 133 126 44 183 832 1014 688 871 .95 90 0 .247 .184 .971 .842 96 92 96 94 1.221 .843 .819 .784 1.676 1.187 1.136 .771 1275 1081 329 52 3440 7740 45 54 187 196 .247
13 406 547 0 188 144 141 32 426 523 397 387 513 0 126 136 126 47 183 575 758 561 743 .83 70 0 .434 .466 .978 .995 100 100 100 100 1.073 .74 .932 .953 1.64 1.351 1.381 .821 823 793 220 32 3590 7740 46 53 203 210 .434
14 39 197 0 45 164 158 45 51 194 59 33 168 0 71 140 135 56 196 86 281 48 243 .24 50 0 .746 .294 1.109 1.277 50 33 41 33 .864 .596 1.157 .846 3.32 1.677 1.226 2.854 110 72 80 12 3730 7710 44 49 218 223 .746
15 108 251 0 72 147 143 34 107 3543 3421 3631 3753 0 1334 130 122 50 177 4958 5135 5262 5439 .73 80 0 5.534 5.607 27.709 29.246 76 69 100 100 .031 .022 31.972 33.62 1.72 46.336 48.725 32.498 3528 3739 281 52 3890 7750 47 55 233 241 5.534
16 1592 1733 0 1213 144 141 31 1701 2433 2307 2146 2272 0 1481 134 126 59 183 3343 3526 3110 3293 .98 100 0 .975 .966 1.596 1.395 98 96 100 100 .737 .509 1.356 1.348 1.794 1.966 1.954 1.305 4008 3738 354 80 4040 7750 46 56 247 257 .975
17 450 589 0 230 140 139 30 445 2942 2823 2904 3023 0 1618 127 119 55 172 4091 4264 4209 4381 .91 100 0 3.201 3.225 6.077 6.2 97 96 100 100 .158 .109 6.344 6.453 1.673 9.194 9.353 7.064 3268 3354 349 80 4190 7740 45 55 262 272 3.201
18 85 228 0 65 143 143 33 93 177 49 28 156 0 78 129 128 44 186 71 257 41 226 .32 80 0 -.389 -1.067 .666 .655 88 63 42 25 1.898 1.31 .527 .329 3.442 .764 .477 .828 142 113 234 52 4320 7740 46 54 276 284 -.389
19 236 386 0 147 155 150 48 244 232 91 89 230 0 64 142 141 45 204 132 336 129 333 .46 70 0 -.888 -.872 .46 .388 87 78 81 50 2.681 1.85 .373 .377 3.403 .541 .547 .302 335 325 213 32 4460 7730 45 52 290 297 -.888
20 322 460 0 156 141 138 31 349 227 106 98 219 0 60 124 121 36 175 154 329 142 317 .54 70 0 -1.184 -1.181 .293 .32 100 100 87 75 3.292 2.272 .304 .304 2.226 .44 .441 .249 455 420 232 32 4610 7740 46 53 305 312 -1.184

Total number of rows: 43008

Table truncated, full table size 9163 Kbytes.




Supplementary data files not provided
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