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Sample GSM6258 Query DataSets for GSM6258
Status Public on Apr 15, 2004
Title AML 96
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 96
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=670650LaserPower=4.584.19
Lot batch = shcz211
 
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
1 126 201 0 87 77 75 21 138 426 352 343 417 0 161 77 74 26 69 329 398 321 390 .84 90 0 1.253 1.347 2.895 2.766 98 86 100 100 .392 .419 2.551 2.722 1.861 2.384 2.544 2.748 490 469 310 52 1900 8310 70 79 25 34 1.253
2 441 516 0 345 77 75 19 487 110 38 36 108 0 35 76 72 26 67 36 103 34 101 .47 80 0 -3.777 -3.712 .107 .114 94 92 63 28 12.816 13.713 .078 .082 2.401 .073 .076 .056 525 477 247 52 2050 8310 71 79 41 49 -3.777
3 242 318 0 283 79 76 22 330 287 210 155 232 0 190 78 77 25 72 196 268 145 217 .94 80 0 -.75 -.74 .632 .6 90 88 88 84 1.571 1.681 .636 .64 1.666 .595 .599 .647 540 397 256 52 2190 8300 70 78 55 63 -.75
4 106 185 0 73 82 79 24 120 196 117 112 191 0 76 81 79 26 74 109 183 105 179 .72 70 0 -.134 -.018 .911 .962 100 81 90 78 1.026 1.097 .975 1.057 2.106 .911 .987 1.008 237 218 225 32 2340 8310 71 78 70 77 -.134
5 18 95 0 25 83 77 33 20 85 11 9 83 0 27 78 74 26 69 10 79 8 78 .17 100 -50 -1.098 1.047 .918 25 6 25 7 1.818 1.945 .55 .5 4.069 .514 .467 .42 31 27 469 80 2500 8310 70 80 85 95 -.96
6 85 162 0 49 78 77 20 86 185 110 94 169 0 89 79 75 29 70 103 173 88 158 .62 60 0 .257 .048 1.206 1.239 93 75 84 68 .782 .837 1.279 1.106 2.796 1.195 1.034 1.711 196 179 154 32 2650 8310 72 78 102 108 .257
7 70 150 0 77 81 80 20 97 336 262 242 316 0 163 79 74 29 69 245 314 226 295 .84 70 0 1.336 1.692 2.824 2.525 87 78 96 96 .37 .396 2.701 3.457 2.056 2.524 3.231 2.47 359 312 222 32 2780 8310 71 78 114 121 1.336
8 65 146 0 46 85 81 31 70 83 8 4 79 0 24 76 75 23 70 7 78 4 74 .28 70 0 -3.227 -4.12 .234 .313 78 53 25 6 8.75 9.363 .114 .062 3.101 .107 .058 .183 78 69 206 32 2940 8300 70 77 130 137 -3.227
9 8 85 0 24 79 77 24 10 81 4 4 81 0 26 78 77 24 72 4 76 4 76 .08 100 -50 -1.098 1.228 1.033 26 6 17 7 2.5 2.675 .4 .5 4.22 .374 .467 1.996 14 12 379 80 3090 8310 70 80 144 154 -1.42
10 122 200 0 100 80 78 23 129 105 27 11 89 0 54 81 78 28 73 25 98 10 83 .47 90 0 -2.354 -3.569 .18 .183 96 88 28 15 4.778 5.112 .209 .09 2.72 .196 .084 .282 156 133 297 52 3220 8320 71 80 157 166 -2.354
11 42 120 0 41 82 78 29 54 95 16 12 91 0 30 81 79 28 74 15 89 11 85 .03 70 0 -1.852 -1.905 .661 .69 68 40 28 6 3.375 3.611 .296 .286 3.608 .277 .267 49.354 70 54 198 32 3380 8300 70 77 174 181 -1.852
12 116 194 0 86 79 78 21 125 189 114 90 165 0 82 77 75 25 70 107 177 84 154 .73 80 0 -.231 -.464 .834 .914 88 84 90 78 1.096 1.173 .912 .776 2.326 .852 .725 .894 239 206 269 52 3510 8300 70 78 187 195 -.231
13 81 156 0 54 78 75 20 91 117 46 29 100 0 53 72 71 23 66 43 109 27 93 .59 70 0 -1.082 -1.579 .448 .536 93 84 56 40 1.978 2.117 .505 .358 2.145 .472 .335 .611 137 110 220 32 3660 8310 71 78 202 209 -1.082
14 6 83 0 29 79 77 21 11 85 10 11 86 0 26 78 75 26 70 9 79 10 80 .06 100 -50 .777 1.307 1.229 26 11 22 5 1.1 1.177 .909 1.833 3.452 .85 1.713 4.239 21 17 358 80 3820 8310 70 80 217 227 -.235
15 118 194 0 64 78 76 20 131 500 424 411 487 0 202 80 76 29 71 396 467 384 455 .85 90 0 1.597 1.703 3.278 3.282 98 92 100 100 .309 .331 3.237 3.483 1.539 3.025 3.255 3.494 555 529 287 52 3950 8310 70 79 230 239 1.597
16 947 1024 0 732 79 77 22 1076 2512 2435 2272 2349 0 1587 82 77 29 72 2276 2348 2123 2195 .97 90 0 1.081 1.165 2.333 2.26 100 100 100 100 .442 .473 2.263 2.399 1.341 2.115 2.242 2.278 3511 3219 289 52 4100 8310 70 79 245 254 1.081
17 144 222 0 211 80 78 23 217 628 552 419 495 0 517 80 76 26 71 516 587 392 463 .93 100 0 1.249 1.443 2.677 2.442 91 88 97 96 .393 .421 2.544 2.91 1.778 2.377 2.719 2.596 769 563 397 80 4250 8300 69 79 260 270 1.249
18 6 83 0 26 79 77 21 10 79 1 -4 74 0 24 82 78 26 73 1 74 69 -1 100 -50 1.009 .952 27 10 15 3 10 10.7 .1 3.87 .093 -1 11 2 396 80 4400 8300 69 79 275 285 -3.42
19 67 142 0 53 79 75 22 74 121 44 35 112 0 39 82 77 28 72 41 113 33 105 .31 70 0 -.848 -1.034 .644 .725 84 71 65 37 1.682 1.8 .595 .522 3.503 .556 .488 .497 118 102 194 32 4560 8300 70 77 292 299 -.848
20 22 99 0 35 81 77 30 27 97 22 18 93 0 36 78 75 30 70 21 91 17 87 .43 100 -50 -.387 .89 1.027 40 16 36 12 1.227 1.313 .815 .818 3.436 .762 .765 1.035 49 40 375 80 4690 8300 69 79 304 314 -.393

Total number of rows: 43008

Table truncated, full table size 8456 Kbytes.




Supplementary data files not provided

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