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Sample GSM6286 Query DataSets for GSM6286
Status Public on Apr 15, 2004
Title AML 107
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 107
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=710640LaserPower=3.974.2
Lot batch = shcz111
 
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 52 87 0 29 36 35 7 50 83 45 46 84 0 39 48 38 28 54 64 119 66 120 .46 60 -100 .338 .988 .873 100 81 65 28 1.111 .778 .9 .885 2.916 1.286 1.264 1.365 95 98 160 32 1550 8530 38 44 24 30 .363
2 158 193 0 198 37 35 10 234 110 72 60 98 0 68 52 38 49 54 103 157 86 140 .8 60 -100 -.882 .276 .273 93 93 53 28 3.25 2.275 .308 .38 2.864 .44 .542 .29 306 218 171 32 1700 8530 38 44 39 45 -1.186
3 247 281 0 265 37 34 11 287 207 171 145 181 0 140 40 36 13 51 244 296 207 259 .87 70 -100 -.254 .775 .582 93 90 96 93 1.678 1.175 .596 .587 2.842 .851 .839 .532 458 392 228 32 1840 8530 37 44 52 59 -.232
4 76 110 0 56 36 34 7 80 386 348 276 314 0 254 42 38 14 54 497 551 394 449 .85 60 0 2.636 2.375 4.174 4.14 87 87 100 96 .23 .161 4.35 3.632 1.932 6.214 5.188 5.053 428 352 171 32 1980 8530 38 44 67 73 2.636
5 48 82 0 52 35 34 6 59 74 36 23 61 0 38 42 38 13 54 51 106 33 87 .56 80 0 -.198 -.547 .653 .598 90 84 61 46 1.639 1.147 .61 .479 3.113 .872 .685 .636 95 71 291 52 2120 8520 36 44 80 88 -.198
6 77 113 0 66 38 36 9 87 74 36 38 76 0 31 43 38 15 54 51 106 54 109 .48 50 0 -.758 -.504 .517 .379 100 83 66 58 2.417 1.692 .414 .494 2.456 .591 .705 .347 123 115 104 12 2270 8520 37 42 96 101 -.758
7 98 132 0 78 36 34 8 102 189 151 105 143 0 134 43 38 15 54 216 270 150 204 .84 60 0 1.081 .614 1.497 1.49 90 90 90 90 .675 .473 1.48 1.071 2.78 2.115 1.531 1.718 253 203 170 32 2420 8520 37 43 111 117 1.081
8 46 81 0 50 36 35 7 63 54 16 15 53 0 21 43 38 14 54 23 77 21 76 .2 70 0 -1.463 -1.102 .4 .377 90 84 50 28 3.938 2.756 .254 .326 5.614 .363 .466 .119 79 61 228 32 2560 8530 37 44 124 131 -1.463
9 71 106 0 52 36 35 8 81 111 73 70 108 0 52 43 38 14 54 104 159 100 154 .74 70 0 .365 .494 .832 .987 100 93 90 81 1.11 .777 .901 .986 2.78 1.287 1.408 .927 154 141 224 32 2710 8520 36 43 139 146 .365
10 45 79 0 55 37 34 12 60 65 25 17 57 0 30 44 40 13 57 36 93 24 81 .62 80 0 -.748 -.89 .448 .571 76 63 59 34 2.4 1.68 .417 .378 3.507 .595 .54 .432 85 62 290 52 2850 8520 36 44 153 161 -.748
11 149 184 0 218 38 35 14 244 107 68 47 86 0 77 43 39 13 56 97 153 67 123 .81 60 0 -1.329 -1.15 .24 .312 90 87 68 56 3.588 2.512 .279 .315 3.045 .398 .451 .276 312 196 176 32 3000 8530 38 44 169 175 -1.329
12 8 43 0 149 38 35 36 67 87 48 9 48 0 106 43 39 13 56 69 124 13 69 .83 100 -50 .684 .941 1 21 17 40 28 1.396 .977 .716 1.125 3.179 1.023 1.607 .587 115 17 438 80 3160 8520 35 45 183 193 .033
13 90 125 0 114 37 35 8 117 78 40 36 74 0 39 42 38 12 54 57 111 51 106 .76 60 0 -1.034 -.807 .47 .351 84 75 75 62 2.925 2.048 .342 .4 3.089 .488 .571 .286 157 126 158 32 3300 8520 37 43 199 205 -1.034
14 33 68 0 33 36 35 7 38 64 26 17 55 0 27 44 38 19 54 37 91 24 79 .47 70 0 -.033 -.442 .523 .614 84 75 43 28 1.462 1.023 .684 .515 3.328 .977 .736 1.038 64 50 228 32 3440 8520 36 43 212 219 -.033
15 89 124 0 75 36 35 7 100 303 263 229 269 0 216 44 40 14 57 376 433 327 384 .92 70 0 1.91 1.878 2.158 2.482 87 84 87 87 .38 .266 2.63 2.573 2.112 3.757 3.676 2.91 363 318 232 32 3580 8520 36 43 226 233 1.91
16 331 366 0 404 36 35 6 407 523 484 415 454 0 426 43 39 13 56 691 747 593 649 .95 80 0 .765 .841 1.418 1.178 92 86 94 90 .841 .589 1.189 1.254 2.483 1.699 1.791 1.115 891 746 293 52 3740 8520 36 44 242 250 .765
17 54 88 0 101 35 34 7 93 405 366 185 224 0 386 44 39 16 56 523 579 264 320 .94 80 0 2.491 2.291 4.261 4.345 86 75 94 90 .254 .178 3.935 3.426 1.824 5.622 4.894 4.089 459 239 274 52 3880 8520 36 44 256 264 2.491
18 56 91 0 33 35 35 6 56 67 30 20 57 0 32 41 37 14 53 43 96 29 81 .36 60 0 -.386 -.971 .501 .506 96 90 62 37 1.867 1.307 .536 .357 3.641 .765 .51 .631 86 76 176 32 4030 8520 37 43 272 278 -.386
19 171 206 0 180 36 35 6 220 109 71 51 89 0 61 42 38 12 54 101 156 73 127 .73 60 0 -1.117 -1.231 .394 .433 93 93 90 84 3.099 2.169 .323 .298 3.419 .461 .426 .255 291 222 171 32 4170 8520 37 43 286 292 -1.117
20 179 214 0 155 36 35 6 216 141 105 105 141 0 78 40 36 10 51 150 201 150 201 .88 60 0 -.526 -.255 .46 .451 96 93 90 84 2.057 1.44 .486 .587 1.719 .694 .838 .455 321 284 170 32 4320 8520 37 43 301 307 -.526

Total number of rows: 43008

Table truncated, full table size 8551 Kbytes.




Supplementary data files not provided
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