NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6336 Query DataSets for GSM6336
Status Public on Apr 15, 2004
Title AML 94
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 94
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=730650LaserPower=4.664.71
Lot batch = shdj103
 
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 GPL319
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
1 572 703 0 330 133 131 30 615 633 468 431 596 0 262 181 165 88 188 532 719 490 677 .9 70 0 -.21 -.224 .735 .775 100 100 100 84 1.314 1.156 .761 .753 1.48 .865 .856 .76 1083 1003 212 32 1510 8490 21 28 23 30 -.21
2 6603 6736 0 3027 135 133 28 6129 3072 2905 3171 3338 0 1616 170 167 58 190 3301 3491 3603 3793 .96 80 0 -.893 -.874 .449 .482 100 100 98 98 2.11 1.857 .474 .48 1.646 .539 .546 .478 9034 9774 284 52 1650 8490 21 29 37 45 -.893
3 1764 1896 0 938 134 132 29 1763 1533 1358 1170 1345 0 811 179 175 66 199 1543 1742 1330 1528 .95 70 0 -.192 -.408 .712 .8 96 96 93 93 1.298 1.142 .77 .663 2.083 .875 .754 .77 3121 2934 212 32 1810 8490 21 28 53 60 -.192
4 603 733 0 519 136 130 40 727 1348 1172 903 1079 0 878 183 176 68 200 1332 1532 1026 1226 .95 80 0 .873 .767 1.549 1.601 98 94 94 92 .62 .546 1.612 1.498 1.702 1.832 1.702 1.686 1899 1506 244 52 1950 8490 21 29 67 75 .873
5 1582 1715 0 1265 136 133 31 1639 1479 1310 1033 1202 0 973 178 169 62 192 1489 1681 1174 1366 .95 80 0 -.139 -.43 .91 .826 96 94 100 94 1.251 1.101 .799 .653 2.003 .908 .742 .767 2949 2615 264 52 2090 8490 21 29 81 89 -.139
6 1300 1439 0 752 137 139 28 1438 1052 868 911 1095 0 462 192 184 60 209 986 1195 1035 1244 .94 60 0 -.544 -.329 .579 .572 93 93 100 96 1.657 1.458 .604 .701 1.531 .686 .796 .584 2306 2211 164 32 2240 8490 22 28 97 103 -.544
7 663 799 0 1377 139 136 32 1249 2922 2746 1460 1636 0 2774 183 176 57 200 3120 3320 1659 1859 .96 100 0 1.321 1.323 2.698 2.356 88 86 98 98 .455 .4 2.199 2.202 2.016 2.498 2.502 2.13 3995 2123 372 80 2390 8490 20 30 110 120 1.321
8 895 1035 0 549 138 140 30 958 435 257 261 439 0 182 185 178 61 202 292 494 297 499 .8 80 0 -1.714 -1.593 .277 .29 96 96 84 75 3.728 3.28 .268 .292 1.725 .305 .331 .255 1215 1156 242 52 2530 8490 21 29 125 133 -1.714
9 670 809 0 371 139 139 30 682 1699 1529 1538 1708 0 783 179 170 63 193 1738 1931 1748 1941 .94 100 0 1.349 1.383 2.362 2.378 100 98 100 100 .446 .393 2.242 2.296 1.567 2.548 2.609 2.269 2211 2208 376 80 2680 8490 20 30 139 149 1.349
10 591 730 0 262 141 139 29 577 523 336 305 492 0 201 194 187 66 213 382 594 347 559 .87 60 0 -.596 -.77 .566 .603 100 96 96 87 1.717 1.511 .582 .516 1.535 .662 .586 .604 913 896 146 32 2820 8490 22 28 155 161 -.596
11 6672 6813 0 4114 145 141 45 6914 1116 929 894 1081 0 664 193 187 69 213 1056 1268 1016 1228 .95 100 0 -2.711 -2.715 .122 .135 100 100 95 86 7.442 6.549 .134 .134 1.663 .153 .152 .137 7843 7566 385 80 2970 8490 20 30 168 178 -2.711
12 8710 8850 0 7664 142 140 30 9705 9043 8856 7634 7821 0 6527 189 187 60 213 10064 10276 8675 8888 .98 100 0 .052 -.006 1.037 .911 100 100 100 100 1.096 .964 .913 .876 1.658 1.037 .996 .882 18561 16344 357 80 3120 8490 20 30 183 193 .052
13 1795 1938 0 868 144 143 29 1717 1256 1072 1012 1196 0 604 186 184 63 209 1218 1427 1150 1359 .96 90 0 -.495 -.642 .605 .59 98 98 98 98 1.602 1.409 .624 .564 1.463 .709 .641 .64 2789 2807 270 52 3260 8480 19 28 197 206 -.495
14 553 695 0 260 146 142 37 546 1771 1589 1522 1704 0 732 187 182 70 207 1806 2013 1730 1936 .95 120 0 1.726 1.645 3.013 3.018 99 98 100 100 .344 .302 2.91 2.752 1.432 3.307 3.128 2.997 2135 2075 464 120 3410 8490 19 31 211 223 1.726
15 1509 1651 0 803 143 142 31 1435 2753 2573 2731 2911 0 1464 184 180 60 205 2924 3128 3103 3308 .97 100 0 1.027 1.04 1.863 1.815 100 98 100 100 .558 .491 1.793 1.81 1.602 2.038 2.057 1.828 4008 4240 316 80 3550 8490 20 30 226 236 1.027
16 8746 8888 0 3978 149 142 79 8724 17073 16885 16801 16989 0 7971 200 188 108 214 19188 19401 19092 19306 .97 110 0 1.137 1.126 1.939 1.884 100 100 100 100 .517 .455 1.935 1.921 1.386 2.199 2.183 1.977 25609 25547 382 80 3700 8490 19 30 240 251 1.137
17 2597 2739 0 778 148 142 77 2312 32879 32694 36590 36775 0 10069 201 185 108 210 37152 37363 41580 41790 .98 120 0 4.006 4.001 14.46 14.183 100 100 100 100 .071 .062 14.141 14.089 1.259 16.069 16.011 14.155 35006 39187 410 120 3850 8490 19 31 255 267 4.006
18 17 156 0 354 138 139 31 158 374 206 77 245 0 371 179 168 63 191 234 425 88 278 .92 100 -50 2.364 1.897 1.548 45 31 52 37 .767 .675 1.304 4.529 2.946 1.482 5.147 1.1 364 94 313 80 3990 8480 19 29 270 280 .567
19 5732 5868 0 2242 138 136 32 5108 2282 2121 2247 2408 0 977 168 161 57 183 2410 2593 2553 2736 .97 100 0 -1.084 -1.167 .414 .408 100 100 100 100 2.408 2.119 .415 .392 1.352 .472 .445 .408 7229 7979 305 80 4140 8490 20 30 285 295 -1.084
20 2823 2962 0 1039 147 139 59 2573 2214 2045 2127 2296 0 806 177 169 69 192 2324 2516 2417 2609 .97 120 0 -.147 -.224 .811 .815 100 100 100 99 1.258 1.107 .795 .753 1.391 .903 .856 .781 4618 4950 426 120 4290 8490 19 31 299 311 -.147

Total number of rows: 43008

Table truncated, full table size 9587 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap