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Sample GSM6236 Query DataSets for GSM6236
Status Public on Apr 15, 2004
Title AML 35
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 35
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=680650LaserPower=4.144.44
Lot batch = shco028
 
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 GPL317
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
1 260 558 0 181 301 298 53 289 429 206 212 435 0 115 228 223 60 297 275 572 283 580 .55 70 0 -.073 .121 .695 .707 87 84 84 71 1.403 1.052 .713 .815 2.964 .95 1.087 .61 495 472 220 32 1840 7880 64 71 60 67 -.073
2 512 823 0 204 310 311 58 429 369 134 145 380 0 68 234 235 52 313 179 492 193 507 .57 60 0 -1.264 -1.405 .32 .327 93 90 90 62 3.201 2.401 .312 .283 2.054 .416 .378 .238 563 657 146 32 2000 7890 66 72 77 83 -1.264
3 2883 3190 0 1590 304 307 52 2871 412 184 161 389 0 148 230 228 50 304 245 549 215 519 .78 110 0 -3.549 -3.747 .071 .072 98 98 81 67 15.603 11.702 .064 .056 2.062 .085 .074 .06 3055 3044 378 80 2120 7890 63 74 86 97 -3.549
4 2828 3117 0 3629 290 289 64 3709 2671 2441 1588 1818 0 2338 236 230 63 307 3255 3561 2117 2424 .94 100 0 -.189 -.418 .75 .632 96 92 96 96 1.519 1.14 .658 .562 2.422 .878 .749 .633 6150 4416 320 80 2270 7900 65 75 102 112 -.189
5 578 851 0 601 288 273 88 721 546 317 243 472 0 221 240 229 75 305 423 728 324 629 .78 70 0 -.77 -.835 .378 .385 81 78 93 68 2.274 1.706 .44 .42 1.96 .586 .561 .346 1038 821 212 32 2430 7890 65 72 119 126 -.77
6 167 448 0 167 285 281 59 159 399 164 187 422 0 131 246 235 76 313 219 532 249 563 .59 70 0 .46 .578 .956 .9 68 59 78 56 .97 .727 1.031 1.12 2.102 1.375 1.493 .931 323 354 195 32 2580 7900 66 73 134 141 .46
7 639 928 0 449 296 289 69 618 1573 1332 1185 1426 0 676 250 241 78 321 1776 2097 1580 1901 .92 80 0 1.523 1.306 2.34 2.085 88 86 100 100 .464 .348 2.155 1.854 1.733 2.874 2.473 1.953 1950 1824 245 52 2720 7890 65 73 148 156 1.523
8 2896 3160 0 2886 274 264 64 3314 2975 2743 2345 2577 0 1965 237 232 58 309 3657 3967 3127 3436 .94 90 0 .142 .111 1.176 .881 92 92 100 100 1.208 .906 .828 .81 2.572 1.104 1.08 .755 6057 5241 264 52 2860 7890 64 73 161 170 .142
9 509 772 0 501 271 263 74 550 3578 3350 2584 2812 0 2693 236 228 59 304 4467 4771 3445 3749 .93 110 0 3.022 2.759 6.524 5.578 77 68 98 98 .164 .123 6.091 5.077 1.773 8.121 6.769 6.105 3900 3093 403 80 3000 7890 63 74 174 185 3.022
10 0 260 0 140 267 260 81 44 281 53 56 284 0 85 228 228 54 304 71 375 75 379 .37 100 -50 .797 .759 28 17 51 23 .83 .623 1.205 3.663 1.606 .513 97 56 322 80 3160 7880 63 73 191 201 .684
11 1815 2096 0 1007 285 281 62 1769 874 646 633 861 0 365 228 228 60 304 861 1165 844 1148 .92 110 0 -1.038 -1.105 .378 .376 98 97 96 92 2.738 2.054 .365 .349 1.973 .487 .465 .335 2415 2448 375 80 3280 7890 63 74 202 213 -1.038
12 948 1253 0 806 312 305 63 1110 799 566 503 736 0 357 238 233 63 311 755 1065 671 981 .92 80 0 -.557 -.499 .531 .491 96 94 100 92 1.961 1.471 .51 .531 1.765 .68 .707 .459 1676 1451 275 52 3450 7890 65 73 221 229 -.557
13 610 899 0 377 331 289 197 634 441 207 185 419 0 154 2281 234 9682 312 276 588 247 559 .64 80 0 -1.2 -1.306 .263 .321 84 71 0 0 3.063 2.297 .326 .303 2.388 .435 .404 .305 841 795 258 52 3590 7890 65 73 235 243 -1.2
14 43 322 0 114 281 279 52 65 262 39 33 256 0 65 231 223 65 297 52 349 44 341 .41 100 -50 .033 .569 .62 46 35 36 7 1.667 1.25 .6 .767 3.205 .8 1.023 .507 104 76 342 80 3740 7880 63 73 249 259 -.322
15 3205 3455 0 2657 260 250 94 3353 1288 1065 826 1049 0 824 226 223 55 297 1420 1717 1101 1399 .94 110 0 -1.24 -1.541 .357 .325 90 88 96 92 3.148 2.361 .318 .258 2.375 .424 .344 .297 4418 4031 430 80 3880 7890 63 74 262 273 -1.24
16 1045 1290 0 614 281 245 182 1139 592 367 329 554 0 205 233 225 73 300 489 789 439 739 .87 70 0 -1.219 -1.252 .344 .323 93 87 93 87 3.104 2.328 .322 .315 1.953 .43 .42 .288 1506 1374 215 32 4030 7870 63 70 279 286 -1.219
17 160 416 0 165 259 256 61 145 310 90 78 298 0 112 226 220 60 293 120 413 104 397 .51 70 0 -.273 -.621 .629 .594 59 56 53 31 1.611 1.208 .621 .488 2.337 .828 .65 .599 235 238 215 32 4180 7890 65 72 294 301 -.273
18 50 301 0 108 254 251 58 66 272 60 41 253 0 78 216 212 55 283 80 363 55 337 .24 100 -50 .129 .708 .586 47 23 38 26 1.1 .825 .909 .82 3.946 1.212 1.093 .478 126 91 349 80 4330 7870 62 72 308 318 .278
19 1146 1417 0 385 274 271 53 1055 499 282 300 517 0 116 219 217 51 289 376 665 400 689 .84 110 0 -1.488 -1.519 .266 .268 100 100 97 91 3.741 2.806 .267 .262 1.643 .356 .349 .246 1337 1446 363 80 4460 7880 62 73 320 331 -1.488
20 276 558 0 337 304 282 113 340 535 315 283 503 0 246 225 220 54 293 420 713 377 671 .77 100 0 .305 .451 1.063 .829 63 53 85 76 1.079 .81 .926 1.025 2.849 1.235 1.367 .731 655 559 343 80 4610 7880 63 73 336 346 .305

Total number of rows: 43008

Table truncated, full table size 9221 Kbytes.




Supplementary data files not provided
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