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Sample GSM6257 Query DataSets for GSM6257
Status Public on Apr 15, 2004
Title AML 45
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 45
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=4.564.49
Lot batch = shcz210
 
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
1 175 269 0 127 96 94 27 185 450 352 316 414 0 210 101 98 34 108 387 495 347 455 .81 90 0 1.064 .989 2.162 1.961 96 84 100 96 .526 .478 1.903 1.806 2.353 2.091 1.984 2.061 537 491 305 52 1880 8230 62 71 23 32 1.064
2 369 464 0 328 105 95 92 470 382 283 270 369 0 139 103 99 36 109 311 420 297 405 .83 80 0 -.596 -.315 .662 .652 96 82 98 96 1.661 1.511 .602 .732 1.818 .662 .804 .457 753 639 266 52 2020 8230 63 71 38 46 -.596
3 352 445 0 322 105 93 94 434 424 333 301 392 0 182 97 91 35 100 366 466 331 431 .89 80 0 -.246 -.09 .853 .843 94 78 96 94 1.303 1.186 .767 .855 1.744 .843 .94 .645 767 653 256 52 2170 8230 63 71 53 61 -.246
4 153 249 0 132 97 96 28 189 155 62 54 147 0 62 96 93 29 102 68 170 59 162 .46 80 0 -1.472 -1.366 .37 .339 90 82 67 48 3.048 2.774 .328 .353 4.25 .36 .388 .236 251 207 258 52 2320 8230 63 71 68 76 -1.472
5 44 137 0 49 96 93 27 46 119 20 13 112 0 44 101 99 32 109 22 131 14 123 .2 100 -50 -1.623 .595 .591 58 40 35 10 2.3 2.093 .435 .295 4.755 .478 .325 .673 66 57 369 80 2470 8230 62 72 82 92 -1.066
6 64 155 0 42 94 91 25 63 162 64 73 171 0 49 100 98 33 108 70 178 80 188 .3 70 0 .159 .326 .99 .943 84 62 71 53 .984 .896 1.016 1.141 3.334 1.116 1.253 1.607 127 137 193 32 2610 8220 62 69 97 104 .159
7 88 182 0 172 96 94 28 126 329 233 154 250 0 358 99 96 32 105 256 362 169 275 .88 90 -100 .943 1.652 1.599 82 61 90 82 .541 .492 1.849 1.75 2.668 2.032 1.923 2.114 359 242 343 52 2760 8230 62 71 111 120 1.023
8 92 186 0 87 99 94 27 101 138 37 30 131 0 56 103 101 30 111 41 152 33 144 .52 80 0 -1.313 -1.481 .513 .579 82 73 46 28 2.73 2.484 .366 .326 3.335 .403 .358 .471 138 122 249 52 2910 8230 63 71 127 135 -1.313
9 56 158 0 51 105 102 31 57 118 18 10 110 0 48 102 100 35 110 20 130 11 121 .03 60 0 -1.527 -2.349 .438 .468 65 40 28 15 3.167 2.882 .316 .179 4.133 .347 .196 .085 75 66 139 32 3040 8200 61 67 141 147 -1.527
10 81 172 0 60 98 91 35 91 115 22 22 115 0 40 99 93 33 102 24 126 24 126 .19 90 0 -1.912 -1.744 .389 .576 82 57 38 11 4.136 3.764 .242 .272 2.947 .266 .298 .163 113 103 363 52 3200 8220 61 70 155 164 -1.912
11 68 162 0 62 104 94 45 82 110 17 8 101 0 35 96 93 29 102 19 121 9 111 .03 70 0 -2.134 -2.951 .398 .47 75 31 31 12 4.824 4.389 .207 .118 4.505 .228 .129 .019 99 76 208 32 3360 8210 61 68 172 179 -2.134
12 201 295 0 152 99 94 25 220 215 117 110 208 0 83 101 98 32 108 129 236 121 229 .7 70 0 -.775 -.734 .47 .616 90 84 84 68 1.88 1.711 .532 .547 2.86 .584 .601 .449 337 311 208 32 3490 8210 61 68 185 192 -.775
13 95 191 0 120 97 96 26 122 161 59 56 158 0 69 102 102 33 112 65 177 62 174 .61 70 0 -.912 -.626 .712 .625 75 75 71 40 2.068 1.882 .484 .589 3.449 .531 .648 .481 181 151 208 32 3640 8200 60 67 200 207 -.912
14 10 104 0 51 95 94 26 20 108 13 9 104 0 54 95 95 30 104 14 119 10 114 .4 100 -50 -.016 1.128 1.183 30 17 26 11 1.538 1.4 .65 .9 3.97 .714 .989 1.591 33 19 350 80 3790 8210 60 70 214 224 -.485
15 179 274 0 236 99 95 29 247 507 414 338 431 0 329 96 93 34 102 455 557 371 474 .91 80 0 .881 1.053 1.909 1.659 88 82 94 88 .597 .543 1.676 1.888 1.98 1.842 2.075 1.564 661 517 241 52 3930 8200 60 68 229 237 .881
16 1032 1127 0 908 98 95 27 1154 1749 1651 1357 1455 0 989 102 98 36 108 1814 1922 1491 1599 .95 90 0 .653 .531 1.645 1.503 98 98 100 100 .699 .636 1.431 1.315 1.569 1.572 1.445 1.284 2805 2389 289 52 4080 8210 60 69 243 252 .653
17 178 275 0 256 101 97 32 267 1756 1655 1264 1365 0 1139 106 101 37 111 1819 1930 1389 1500 .91 90 0 2.768 2.964 7.252 6.207 92 84 100 100 .161 .147 6.199 7.101 1.908 6.812 7.803 5.66 1922 1442 343 52 4220 8200 59 68 257 266 2.768
18 33 128 0 49 95 95 24 41 111 15 1 97 0 45 96 96 32 105 16 122 1 107 .06 80 0 -1.315 -4.908 .741 .702 51 34 25 17 2.733 2.487 .366 .03 4.949 .402 .033 1.278 56 34 254 52 4380 8200 60 68 274 282 -1.315
19 70 165 0 78 96 95 26 87 131 38 32 125 0 45 96 93 31 102 42 144 35 137 .24 90 0 -1.059 -.993 .544 .656 82 67 50 26 2.289 2.083 .437 .457 3.57 .48 .502 .249 125 102 307 52 4520 8190 58 67 287 296 -1.059
20 120 219 0 77 105 99 42 117 112 17 15 110 0 37 98 95 34 104 19 123 16 121 .14 60 0 -2.647 -2.864 .287 .321 78 62 37 6 6.882 6.263 .145 .125 3.187 .16 .137 .103 134 135 165 32 4660 8200 61 67 303 309 -2.647

Total number of rows: 43008

Table truncated, full table size 8867 Kbytes.




Supplementary data files not provided
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