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Sample GSM6282 Query DataSets for GSM6282
Status Public on Apr 15, 2004
Title AML 88
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 88
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=690650LaserPower=4.014.45
Lot batch = shcz226
 
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 49 85 0 52 38 36 9 55 533 498 397 432 0 414 39 35 14 42 593 635 473 514 .9 100 0 3.43 3.27 8.758 8.483 76 67 98 98 .11 .093 9.055 8.102 2.079 10.779 9.645 9.159 553 446 433 80 2030 7670 42 52 30 40 3.43
2 580 617 0 573 38 37 10 696 124 86 61 99 0 75 41 38 13 45 102 148 73 118 .89 80 0 -2.765 -2.998 .131 .125 98 96 86 71 8.093 6.798 .124 .105 2.267 .147 .125 .115 782 641 242 52 2170 7670 43 51 45 53 -2.765
3 345 381 0 274 38 36 11 345 193 155 126 164 0 126 41 38 14 45 185 230 150 195 .91 80 0 -.903 -1.202 .492 .488 98 92 92 84 2.226 1.87 .449 .365 2.112 .535 .435 .425 500 471 263 52 2320 7670 43 51 60 68 -.903
4 160 196 0 75 38 36 11 155 72 34 30 68 0 29 42 38 16 45 40 86 36 81 .57 60 0 -1.937 -2.163 .238 .245 96 93 65 43 4.559 3.829 .219 .188 2.493 .261 .223 .192 189 190 170 32 2470 7660 43 49 76 82 -1.937
5 135 172 0 97 39 37 10 136 146 108 81 119 0 87 42 38 15 45 129 174 96 142 .85 90 0 -.081 -.485 .919 .854 90 88 88 82 1.259 1.058 .794 .6 2.327 .945 .714 .812 244 216 330 52 2620 7670 42 51 89 98 -.081
6 120 157 0 69 39 37 10 124 143 104 87 126 0 73 42 39 15 46 124 170 104 150 .87 70 0 -.002 -.212 .752 .848 93 90 90 87 1.192 1.002 .839 .725 1.939 .998 .863 .937 228 207 212 32 2760 7660 42 49 104 111 -.002
7 179 216 0 126 39 37 10 167 275 237 222 260 0 174 42 38 15 45 282 327 264 310 .92 80 0 .757 .562 1.52 1.507 88 82 86 86 .705 .592 1.419 1.24 1.956 1.689 1.476 1.434 404 401 277 52 2900 7670 43 51 118 126 .757
8 105 142 0 69 39 37 10 104 91 53 55 93 0 43 41 38 15 45 63 108 65 111 .77 80 0 -.721 -.681 .476 .516 84 80 75 61 1.962 1.648 .51 .524 1.948 .607 .624 .497 157 160 279 52 3050 7670 43 51 133 141 -.721
9 55 93 0 40 40 38 11 58 66 28 22 60 0 21 42 38 15 45 33 79 26 71 .4 60 0 -.799 -1.07 .463 .443 90 78 65 37 2.071 1.74 .483 .4 2.766 .575 .476 .379 86 77 164 32 3200 7660 43 49 149 155 -.799
10 83 122 0 62 42 39 15 85 54 15 7 46 0 24 42 39 15 46 18 64 8 55 .36 90 0 -2.251 -3.316 .205 .269 82 80 40 30 5.667 4.76 .176 .084 3.352 .21 .1 .166 100 90 354 52 3350 7670 42 51 162 171 -2.251
11 415 456 0 233 44 41 18 425 119 78 66 107 0 58 45 41 17 49 93 142 79 127 .83 60 0 -2.194 -2.401 .169 .192 93 93 87 75 5.449 4.577 .184 .159 2.047 .218 .189 .176 503 481 166 32 3500 7660 43 49 179 185 -2.194
12 385 424 0 346 40 39 10 436 544 505 418 457 0 314 43 39 16 46 601 648 498 544 .93 60 0 .463 .37 1.45 1.156 100 96 100 100 .863 .725 1.158 1.086 2.228 1.379 1.293 1.052 941 803 166 32 3630 7660 43 49 192 198 .463
13 154 190 0 86 39 36 19 155 315 276 304 343 0 161 42 39 15 46 329 375 362 408 .88 70 0 1.084 1.233 1.778 1.984 96 93 100 100 .562 .472 1.781 1.974 1.646 2.12 2.35 1.921 431 458 231 32 3780 7660 42 49 206 213 1.084
14 58 95 0 21 38 37 9 60 93 52 45 86 0 25 41 41 12 49 62 111 54 102 .54 50 0 .045 -.115 .819 .744 100 100 100 91 1.154 .969 .867 .776 1.939 1.032 .924 .931 112 103 104 12 3930 7660 43 48 222 227 .045
15 62 100 0 51 39 38 9 64 2693 2654 2432 2471 0 1591 43 39 17 46 3160 3206 2895 2942 .89 80 0 5.625 5.545 37.572 40.667 82 76 100 100 .024 .02 41.469 39.226 1.631 49.368 46.697 40.299 2718 2494 297 52 4070 7660 42 50 235 243 5.625
16 885 923 0 675 39 38 10 893 1404 1365 1542 1581 0 888 43 39 17 46 1625 1671 1836 1882 .97 90 0 .864 1.053 1.968 1.578 94 92 100 96 .654 .55 1.529 1.742 2.198 1.82 2.074 1.452 2258 2427 332 52 4230 7660 41 50 250 259 .864
17 111 149 0 133 39 38 9 143 1173 1134 1263 1302 0 841 43 39 15 46 1350 1396 1504 1550 .94 90 0 3.239 3.76 8.949 8.03 82 76 98 98 .126 .106 7.93 11.378 2.131 9.441 13.546 7.37 1277 1374 324 52 4370 7660 41 50 264 273 3.239
18 73 112 0 32 40 39 10 71 55 15 13 53 0 23 44 40 15 48 18 65 15 63 .37 60 0 -1.991 -2.238 .274 .319 96 93 43 12 4.733 3.976 .211 .178 2.328 .252 .212 .231 86 86 170 32 4520 7660 43 49 281 287 -1.991
19 294 334 0 160 43 40 15 283 160 121 133 172 0 68 45 39 17 46 144 190 158 205 .88 60 0 -.974 -.893 .462 .428 96 96 93 87 2.339 1.965 .428 .452 2.114 .509 .539 .392 404 427 166 32 4670 7660 43 49 296 302 -.974
20 240 279 0 135 45 39 18 225 147 103 102 146 0 48 47 44 17 52 123 175 121 174 .88 50 0 -.876 -.983 .508 .417 100 100 100 91 2.184 1.835 .458 .425 1.769 .545 .506 .5 328 342 98 12 4790 7650 42 47 308 313 -.876

Total number of rows: 43008

Table truncated, full table size 8542 Kbytes.




Supplementary data files not provided

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