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Sample GSM6260 Query DataSets for GSM6260
Status Public on Apr 15, 2004
Title AML 85
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 85
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=750630LaserPower=3.534.65
Lot batch = shcz063
 
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
1 212 327 0 157 117 115 26 250 459 316 294 437 0 236 152 143 56 207 458 665 426 633 .79 90 0 .873 1.007 1.082 1.275 96 94 84 73 .791 .546 1.264 1.387 2.851 1.832 2.01 1.548 566 506 325 52 1550 8230 58 67 30 39 .873
2 2381 2498 0 1826 119 117 30 2606 278 138 114 254 0 125 149 140 57 203 200 403 165 368 .65 90 0 -3.704 -3.849 .069 .059 92 92 75 50 18.884 13.03 .053 .048 3.08 .077 .069 .043 2744 2495 301 52 1690 8240 59 68 44 53 -3.704
3 546 663 0 396 121 117 29 619 398 253 236 381 0 176 149 145 55 210 367 577 342 552 .8 80 0 -.755 -.675 .4 .417 96 92 86 76 2.447 1.688 .409 .432 2.448 .592 .626 .374 872 782 253 52 1840 8240 60 68 60 68 -.755
4 231 348 0 143 120 117 27 240 185 39 32 178 0 69 150 146 54 212 57 268 46 258 .31 80 0 -2.086 -2.316 .274 .301 94 92 42 15 6.154 4.246 .163 .139 3.973 .236 .201 .167 279 263 275 52 1990 8230 59 67 75 83 -2.086
5 181 297 0 109 122 116 28 192 232 87 87 232 0 78 151 145 52 210 126 336 126 336 .53 80 0 -.607 -.522 .439 .483 94 90 67 32 2.207 1.523 .453 .481 2.77 .657 .697 .442 279 268 287 52 2130 8230 59 67 89 97 -.607
6 327 443 0 217 122 116 29 373 261 116 94 239 0 118 152 145 56 210 168 378 136 346 .55 60 0 -1.15 -1.263 .346 .354 96 93 65 40 3.216 2.219 .311 .287 3.485 .451 .417 .287 489 421 150 32 2280 8240 61 67 105 111 -1.15
7 297 412 0 207 119 115 30 313 899 743 590 746 0 579 165 156 66 226 1077 1303 855 1081 .85 90 0 1.783 1.526 2.343 2.314 88 88 96 90 .421 .291 2.374 1.987 2.322 3.44 2.879 2.816 1056 887 312 52 2420 8240 59 68 117 126 1.783
8 328 446 0 153 125 118 58 341 295 142 138 291 0 118 162 153 71 222 206 428 200 422 .48 70 0 -.729 -.714 .441 .396 96 93 71 50 2.401 1.657 .416 .421 2.906 .604 .61 .354 483 466 205 32 2560 8230 59 66 132 139 -.729
9 198 311 0 59 115 113 36 198 220 72 76 224 0 68 153 148 62 214 104 319 110 325 .43 50 0 -.924 -.846 .414 .487 100 100 50 25 2.75 1.898 .364 .384 1.838 .527 .556 .668 270 274 104 12 2710 8230 60 65 148 153 -.924
10 210 323 0 120 115 113 30 211 170 27 14 157 0 63 150 143 58 207 39 246 20 228 .2 80 0 -2.431 -3.372 .227 .259 94 92 28 9 7.815 5.392 .128 .067 2.957 .185 .097 .117 238 224 287 52 2850 8240 60 68 161 169 -2.431
11 226 336 0 116 116 110 30 252 229 83 80 226 0 78 152 146 57 212 120 332 116 328 .32 70 0 -1.067 -.963 .337 .438 100 96 56 31 3.036 2.095 .329 .354 3.232 .477 .513 .259 335 306 226 32 3000 8240 60 67 176 183 -1.067
12 364 481 0 262 121 117 32 372 359 213 183 329 0 150 153 146 58 212 309 520 265 477 .73 80 0 -.269 -.457 .56 .595 88 84 88 71 1.746 1.205 .573 .503 2.202 .83 .729 .517 585 547 292 52 3160 8240 60 68 192 200 -.269
13 241 354 0 139 117 113 27 254 349 206 215 358 0 121 149 143 54 207 299 506 312 519 .65 70 0 .233 .371 .81 .829 96 93 87 81 1.233 .851 .811 .892 2.23 1.175 1.293 .872 460 456 196 32 3310 8240 60 67 207 214 .233
14 124 238 0 80 119 114 39 134 280 132 105 253 0 111 156 148 65 214 191 406 152 367 .68 50 0 .514 .295 1.256 .972 91 66 83 33 1.015 .7 .985 .847 2.775 1.428 1.227 1.393 266 229 92 12 3440 8250 62 67 221 226 .514
15 100 215 0 112 117 115 32 134 713 567 483 629 0 346 151 146 60 212 822 1033 700 912 .47 90 0 2.616 2.807 4.27 4.627 84 75 100 96 .236 .163 4.231 4.83 2.903 6.132 7 7.166 701 583 360 52 3580 8230 58 67 233 242 2.616
16 1011 1130 0 829 120 119 29 1236 1333 1177 1061 1217 0 593 159 156 57 226 1706 1932 1538 1764 .92 80 0 .465 .605 .969 1.017 98 98 98 98 1.05 .725 .952 1.049 1.654 1.38 1.521 .826 2413 2072 304 52 3740 8230 59 67 250 258 .465
17 264 380 0 168 119 116 27 283 1624 1470 1317 1471 0 782 157 154 58 223 2130 2354 1909 2132 .89 90 0 2.912 2.854 5.194 4.905 96 96 100 100 .193 .133 5.194 4.989 1.601 7.528 7.23 4.924 1753 1581 300 52 3890 8230 58 67 264 273 2.912
18 23 137 0 60 115 114 26 32 170 24 10 156 0 70 153 146 62 212 35 246 14 226 .28 100 -50 -.666 1.061 1.042 43 31 26 8 1.333 .92 .75 .435 3.89 1.087 .63 3.438 56 33 394 80 4040 8230 58 68 279 289 .12
19 204 321 0 124 117 117 27 219 252 112 98 238 0 108 149 140 59 203 162 365 142 345 .48 60 0 -.432 -.522 .532 .58 96 96 71 40 1.955 1.349 .511 .48 2.273 .741 .696 .448 331 302 158 32 4180 8240 61 67 295 301 -.432
20 181 292 0 66 124 111 58 183 245 89 116 272 0 68 161 156 69 226 129 355 168 394 .41 50 0 -.505 -.107 .531 .649 100 83 58 33 2.056 1.419 .486 .641 2.541 .705 .929 .709 272 297 104 12 4330 8230 60 65 310 315 -.505

Total number of rows: 43008

Table truncated, full table size 8846 Kbytes.




Supplementary data files not provided
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