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Sample GSM6259 Query DataSets for GSM6259
Status Public on Apr 15, 2004
Title AML 13
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 13
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=720640LaserPower=3.514.67
Lot batch = shcz062
 
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
1 301 410 0 195 114 109 31 332 301 169 145 277 0 96 140 132 54 163 209 372 179 342 .73 90 0 -.67 -.75 .508 .526 94 90 94 61 1.964 1.591 .509 .482 2.11 .628 .595 .462 501 446 349 52 1550 8240 59 68 30 39 -.67
2 2023 2135 0 1302 118 112 35 2030 621 487 467 601 0 305 142 134 54 165 601 767 577 742 .91 80 0 -1.755 -1.811 .265 .25 98 96 96 84 4.168 3.376 .24 .231 1.973 .296 .285 .221 2517 2490 254 52 1700 8240 60 68 46 54 -1.755
3 756 870 0 233 123 114 51 760 636 501 476 611 0 199 145 135 66 167 619 785 588 754 .91 70 0 -.297 -.363 .627 .684 100 100 96 96 1.517 1.229 .659 .63 1.592 .814 .777 .622 1261 1232 221 32 1840 8240 60 67 60 67 -.297
4 273 389 0 132 119 116 35 289 212 77 75 210 0 63 143 135 52 167 95 262 93 259 .34 70 0 -1.604 -1.56 .264 .276 96 93 62 25 3.753 3.04 .266 .275 2.681 .329 .339 .151 366 348 219 32 1990 8240 60 67 75 82 -1.604
5 172 289 0 118 122 117 34 202 242 104 67 205 0 92 145 138 49 170 128 299 83 253 .53 80 0 -.654 -1.056 .471 .51 98 90 73 38 1.942 1.573 .515 .39 3.215 .636 .481 .544 306 239 270 52 2140 8230 59 67 90 98 -.654
6 353 466 0 195 120 113 36 380 252 115 112 249 0 68 142 137 47 169 142 311 138 307 .63 70 0 -1.42 -1.352 .314 .297 96 96 84 56 3.304 2.677 .303 .317 2.102 .374 .392 .272 495 465 200 32 2280 8240 60 67 104 111 -1.42
7 294 406 0 113 119 112 35 310 493 363 303 433 0 207 138 130 50 160 448 609 374 535 .76 70 0 .532 .348 1.013 .996 100 100 96 93 .854 .692 1.171 1.031 2.17 1.446 1.272 1.327 673 597 227 32 2420 8230 59 66 118 125 .532
8 160 273 0 125 118 113 35 174 243 111 103 235 0 83 138 132 49 163 137 300 127 290 .54 80 0 -.345 -.331 .611 .606 86 80 78 51 1.568 1.27 .638 .644 2.193 .788 .795 .614 285 263 248 52 2580 8240 60 68 134 142 -.345
9 81 188 0 62 111 107 29 90 211 74 72 209 0 74 143 137 51 169 91 260 89 258 .54 80 0 .022 .134 .755 .987 90 69 57 32 1.216 .985 .822 .889 3.053 1.015 1.097 1.473 164 153 256 52 2720 8230 59 67 148 156 .022
10 176 284 0 86 113 108 32 179 181 46 46 181 0 70 138 135 50 167 57 223 57 223 .31 90 0 -1.656 -1.632 .325 .396 98 94 48 25 3.891 3.152 .257 .261 2.927 .317 .323 .354 225 222 336 52 2870 8230 58 67 162 171 -1.656
11 157 264 0 98 113 107 32 184 180 49 51 182 0 66 134 131 48 162 60 222 63 225 .18 70 0 -1.605 -1.318 .455 .464 100 100 50 21 3.755 3.042 .266 .325 2.014 .329 .401 .158 233 208 210 32 3020 8230 59 66 178 185 -1.605
12 863 968 0 899 106 105 37 1013 701 577 435 559 0 446 131 124 47 153 712 865 537 690 .89 70 0 -.508 -.684 .629 .591 96 93 96 96 1.756 1.422 .57 .504 1.802 .703 .622 .466 1590 1298 232 32 3170 8240 60 67 193 200 -.508
13 282 383 0 228 104 101 42 321 338 212 206 332 0 105 138 126 67 156 262 417 254 410 .71 60 0 -.295 -.149 .732 .569 90 90 93 75 1.514 1.226 .66 .73 2.173 .815 .902 .502 533 488 171 32 3310 8240 61 67 208 214 -.295
14 25 131 0 57 109 106 63 30 201 79 74 196 0 78 134 122 73 151 98 248 91 242 .27 100 -50 1.87 2.058 1.633 17 2 50 15 .38 .308 2.633 2.96 3.232 3.251 3.654 4.286 109 99 360 80 3460 8230 58 68 221 231 1.701
15 160 274 0 120 116 114 29 187 1149 1019 884 1014 0 557 133 130 55 160 1258 1419 1091 1252 .86 80 0 2.75 2.77 5.851 5.718 98 88 100 98 .184 .149 5.449 5.525 1.707 6.727 6.821 5.701 1206 1044 237 52 3600 8230 59 67 236 244 2.75
16 2064 2173 0 1253 113 109 54 2004 2340 2213 2114 2241 0 1210 138 127 67 157 2732 2889 2610 2767 .95 90 0 .447 .339 1.334 1.095 96 90 98 98 .906 .734 1.104 1.024 1.895 1.363 1.264 1.031 4217 4178 288 52 3740 8230 58 67 249 258 .447
17 400 503 0 373 125 103 255 494 2298 2170 1999 2127 0 1331 148 128 149 158 2679 2837 2468 2626 .74 90 0 2.439 2.625 5.065 4.496 75 42 98 94 .228 .184 4.393 4.998 1.86 5.423 6.17 3.931 2664 2399 348 52 3890 8230 58 67 264 273 2.439
18 110 218 0 100 112 108 33 123 202 75 67 194 0 73 132 127 52 157 93 249 83 240 .37 70 0 -.41 -.411 .612 .649 84 68 56 15 1.64 1.328 .61 .609 2.778 .753 .752 .626 198 177 214 32 4050 8230 59 66 281 288 -.41
19 271 383 0 171 117 112 33 293 241 105 100 236 0 73 142 136 53 168 130 298 123 291 .58 70 0 -1.177 -1.134 .358 .401 93 93 75 46 2.79 2.26 .358 .369 3.327 .442 .456 .311 398 371 209 32 4180 8230 59 66 294 301 -1.177
20 143 252 0 118 114 109 32 140 223 90 69 202 0 81 140 133 50 164 111 275 85 249 .43 80 0 -.333 -.747 .658 .501 82 65 67 36 1.556 1.26 .643 .483 3.067 .794 .596 .634 230 212 265 52 4330 8240 60 68 309 317 -.333

Total number of rows: 43008

Table truncated, full table size 9122 Kbytes.




Supplementary data files not provided
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