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Sample GSM6277 Query DataSets for GSM6277
Status Public on Apr 15, 2004
Title AML 29
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 29
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=650640LaserPower=4.265.31
Lot batch = shcz221
 
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
1 102 148 0 60 49 46 19 94 330 286 313 357 0 148 46 44 14 44 283 327 310 353 .88 90 0 1.591 1.603 3.148 3 84 80 94 92 .329 .332 3.043 3.069 1.862 3.012 3.038 3.088 380 415 346 52 1920 7800 47 56 27 36 1.591
2 261 308 0 457 49 47 14 432 1716 1672 1042 1086 0 1643 45 44 13 44 1655 1699 1032 1075 .99 100 0 1.938 1.983 4.554 4.019 86 81 100 98 .258 .261 3.87 3.992 1.647 3.832 3.953 3.746 2104 1303 364 80 2060 7800 47 57 41 51 1.938
3 441 488 0 339 49 47 13 422 415 370 335 380 0 282 48 45 14 45 366 411 332 376 .97 90 0 -.204 -.411 .928 .897 92 90 94 92 1.141 1.152 .877 .76 1.677 .868 .752 .849 792 776 327 52 2210 7790 46 55 56 65 -.204
4 86 133 0 104 50 47 16 127 143 96 71 118 0 88 49 47 15 47 95 142 70 117 .86 80 0 -.418 -.291 .682 .693 88 76 75 67 1.323 1.336 .756 .826 2.368 .748 .817 .771 223 157 266 52 2360 7800 48 56 72 80 -.418
5 146 194 0 96 50 48 17 138 181 134 131 178 0 88 48 47 14 47 133 179 130 176 .87 90 0 -.057 -.171 1.096 1 90 80 94 82 1.03 1.04 .971 .897 2.237 .961 .888 .883 272 277 314 52 2500 7800 47 56 85 94 -.057
6 168 214 0 79 50 46 17 156 211 163 168 216 0 97 49 48 16 48 161 209 166 214 .92 70 0 .049 -.014 1.052 .99 90 90 100 96 .957 .967 1.045 1 1.877 1.035 .99 1.102 319 336 213 32 2650 7790 47 54 101 108 .049
7 223 271 0 168 50 48 15 216 530 485 467 512 0 371 48 45 15 45 480 525 462 507 .96 80 0 1.153 1.052 2.033 2.219 88 80 92 88 .445 .45 2.245 2.094 2.141 2.223 2.073 2.278 701 690 289 52 2790 7790 47 55 115 123 1.153
8 120 168 0 57 51 48 18 119 76 32 21 65 0 32 47 44 16 44 32 75 21 64 .53 70 0 -1.909 -2.529 .248 .32 93 93 53 40 3.719 3.756 .269 .175 2.571 .266 .173 .254 151 141 224 32 2940 7790 47 54 130 137 -1.909
9 92 139 0 53 49 47 14 92 251 206 212 257 0 118 47 45 14 45 204 249 210 254 .86 60 0 1.149 1.19 2.205 2.147 96 87 96 93 .447 .451 2.239 2.304 1.476 2.217 2.282 2.344 298 304 170 32 3100 7790 48 54 147 153 1.149
10 109 159 0 37 54 50 19 101 62 17 16 61 0 16 46 45 14 45 17 61 16 60 .44 70 0 -2.585 -2.783 .186 .186 100 93 53 25 5.941 6.001 .168 .147 1.911 .167 .145 .162 118 125 216 32 3240 7790 47 54 160 167 -2.585
11 668 720 0 353 59 52 32 582 140 94 107 153 0 70 49 46 17 46 93 139 106 151 .9 60 0 -2.645 -2.657 .17 .171 87 87 84 71 6.191 6.253 .162 .16 1.821 .16 .159 .162 676 775 160 32 3380 7780 47 53 175 181 -2.645
12 620 668 0 444 51 48 15 629 1067 1021 1048 1094 0 716 50 46 19 46 1011 1056 1038 1083 .98 70 0 .684 .743 1.659 1.617 96 93 100 96 .616 .622 1.623 1.69 1.295 1.607 1.674 1.598 1650 1668 222 32 3520 7790 47 54 188 195 .684
13 200 246 0 102 48 46 14 182 189 146 158 201 0 77 46 43 13 43 145 187 156 199 .92 60 0 -.332 -.354 .782 .755 87 87 96 93 1.247 1.259 .802 .79 1.635 .794 .782 .778 328 358 170 32 3670 7790 48 54 204 210 -.332
14 52 97 0 26 46 45 11 57 71 27 28 72 0 13 45 44 16 44 27 70 28 71 .57 50 0 -1.092 -.907 .459 .439 100 100 75 33 2.111 2.132 .474 .538 2.139 .469 .533 .542 84 80 90 12 3810 7780 47 52 218 223 -1.092
15 220 266 0 111 47 46 12 190 241 197 216 260 0 115 47 44 16 44 195 239 214 257 .93 80 0 .038 -.041 .957 1.021 90 84 92 88 .964 .974 1.037 .982 1.572 1.027 .972 1.017 387 436 284 52 3960 7790 47 55 232 240 .038
16 1063 1110 0 464 49 47 13 846 2080 2035 2500 2545 0 1112 49 45 20 45 2015 2059 2475 2520 .99 90 0 1.252 1.219 2.432 2.376 96 96 100 100 .416 .42 2.405 2.352 1.345 2.382 2.329 2.413 2881 3563 338 52 4110 7780 45 54 246 255 1.252
17 241 288 0 116 48 47 12 224 1477 1432 1578 1623 0 635 47 45 15 45 1418 1462 1562 1607 .96 90 0 2.662 2.697 6.426 6.275 94 94 100 100 .156 .158 6.393 6.548 1.287 6.33 6.483 6.324 1656 1819 300 52 4260 7790 46 55 261 270 2.662
18 17 65 0 47 51 48 17 34 49 6 3 46 0 16 46 43 16 43 6 49 3 46 .2 100 -50 -2.517 .399 .395 50 43 21 8 5.667 5.723 .176 .176 4.04 .175 .175 .127 40 20 348 80 4400 7780 45 55 275 285 -2.517
19 278 328 0 262 53 50 18 310 280 236 193 237 0 204 48 44 16 44 234 277 191 235 .96 80 0 -.408 -.541 .759 .755 86 80 88 84 1.314 1.327 .761 .694 2.065 .754 .687 .759 546 471 255 52 4530 7770 45 53 289 297 -.408
20 296 343 0 186 49 47 13 290 457 410 409 456 0 273 49 47 15 47 406 452 405 451 .97 60 0 .485 .452 1.422 1.343 93 87 96 93 .707 .714 1.414 1.382 1.849 1.4 1.368 1.456 700 705 165 32 4690 7780 47 53 306 312 .485

Total number of rows: 43008

Table truncated, full table size 8698 Kbytes.




Supplementary data files not provided
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