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Sample GSM159228 Query DataSets for GSM159228
Status Public on Aug 28, 2007
Title Normal Colon 1 Top vs. common reference
Sample type RNA
 
Channel 1
Source name amplified SRF
Organism Homo sapiens
Characteristics amplified SRF
LabeledExtract: 56356.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name HKCoN-1A
Organism Homo sapiens
Characteristics HKCoN-1A
LabeledExtract: 56356.Channel_2
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Xin,,Chen
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 10:55:16; Parameter PMT Volts = 510; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 92101; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 10:55:16; Parameter PMT Volts = 790; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 91935; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83872]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen
Description Simple annotation: Colon, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56356.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 29, 2007
Last update date Aug 28, 2007
Contact name Xin Chen
E-mail(s) [email protected]
Phone (415) 502-6526
Fax (415) 502-4332
Organization name UCSF
Street address
City San Francisco
State/province CA
ZIP/Postal code 94143-0446
Country USA
 
Platform ID GPL4788
Series (1)
GSE6894 Normal colon top vs colon crypts

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
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.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 625 1896 181 846 444 1050 637 1840 181 840 456 994 0 0 109 378 40 211 100 100 100 96 1494 1450 .423 2.365 2.18 2.283 2.212 1.442 32 224 3.051 .674 70 1990 5310 47 54 83 90 0 1226 547 679 1.529 1190 643 .654 1.409 .613 .495
2 13581 5854 179 835 13402 5019 14035 6029 185 838 13856 5194 0 0 6973 2248 54 223 100 100 100 100 18421 19050 2.67 .374 .375 .39 .376 1.384 52 276 .356 .941 80 2130 5310 47 55 97 105 0 3785 540 3245 .242 3898 3358 4.13 .242 -2.046 -2.045
3 8131 8398 177 820 7954 7578 7819 8995 185 833 7642 8175 0 0 5561 4104 55 228 94 94 88 90 15532 15817 1.05 .953 1.07 1.153 1.11 1.737 52 272 .867 .885 80 2270 5310 47 55 111 119 0 5430 530 4900 .616 5816 5286 1.623 .692 -.699 -.532
4 1619 1465 208 809 1411 656 1287 1353 208 835 1079 544 0 0 711 470 47 237 100 84 100 65 2067 1623 2.151 .465 .504 .437 .419 2.23 32 176 .466 .48 60 2430 5310 48 54 128 134 0 947 523 424 .301 875 352 3.326 .326 -1.734 -1.617
5 995 8316 209 804 786 7512 1068 8948 210 840 859 8144 0 0 363 3057 43 240 96 98 96 98 8298 9003 .105 9.557 9.481 9.92 9.214 1.61 52 286 9.527 .928 80 2580 5310 47 55 142 150 0 5377 520 4857 6.18 5786 5266 .162 6.13 2.628 2.616
6 694 1234 181 815 513 419 682 1170 193 830 501 355 0 0 127 356 97 234 100 68 100 43 932 856 1.224 .817 .709 .742 .868 2.086 32 218 1.302 .373 70 2720 5310 47 54 156 163 0 798 527 271 .528 757 230 1.894 .458 -.921 -1.126
7 918 4528 178 831 740 3697 919 4493 188 841 741 3662 0 0 397 1747 84 263 98 98 90 98 4437 4403 .2 4.996 4.942 5.168 5.321 1.466 52 290 5.215 .87 80 2870 5310 47 55 171 179 0 2928 537 2390 3.23 2905 2368 .31 3.195 1.692 1.676
8 1445 2824 190 830 1255 1994 1362 2805 217 893 1172 1975 0 0 409 604 143 436 100 100 100 96 3249 3147 .629 1.589 1.685 1.586 1.519 1.346 32 213 1.885 .798 70 3010 5300 46 53 185 192 0 1826 537 1289 1.027 1814 1277 .973 1.09 .039 .124
9 1224 1489 190 859 1034 630 1216 1471 217 906 1026 612 0 0 295 418 141 433 100 61 100 23 1664 1638 1.641 .609 .596 .549 .652 1.796 52 329 1.358 .273 90 3160 5310 46 55 199 208 0 963 555 407 .394 951 396 2.538 .386 -1.344 -1.374
10 1466 2831 180 811 1286 2020 1478 2797 189 840 1298 1986 0 0 259 542 58 419 100 100 100 100 3306 3284 .637 1.571 1.53 1.546 1.585 1.291 52 264 1.708 .872 80 3300 5310 47 55 214 222 0 1831 524 1306 1.016 1809 1284 .985 .989 .022 -.015
11 7857 2067 186 796 7671 1271 7939 2075 1172 1516 7753 1279 0 0 1026 378 6965 5486 73 0 0 0 8942 9032 6.035 .166 .165 .159 .169 1.383 52 276 .724 .769 80 3450 5310 47 55 229 237 0 1337 515 822 .107 1342 827 9.334 .107 -3.223 -3.229
12 6520 38221 180 768 6340 37453 7119 39862 222 808 6939 39094 0 5 3399 17981 383 274 98 100 90 100 43793 46033 .169 5.907 5.634 6.201 6.139 1.217 52 275 5.815 .968 80 3600 5310 47 55 244 252 0 24714 497 24217 3.82 25775 25278 .262 3.643 1.933 1.865
13 2343 21262 182 782 2161 20480 2557 22904 196 829 2375 22122 0 0 659 5006 118 254 100 100 100 100 22641 24497 .106 9.477 9.315 9.708 9.704 1.163 52 266 9.54 .889 80 3740 5310 47 55 258 266 0 13748 506 13242 6.128 14810 14304 .163 6.023 2.615 2.59
14 1125 6398 186 829 939 5569 1095 6400 194 859 909 5571 0 0 284 1654 61 303 100 100 100 100 6508 6480 .169 5.931 6.129 5.907 5.852 1.201 52 264 5.897 .937 80 3890 5310 47 55 273 281 0 4137 536 3601 3.835 4138 3602 .261 3.963 1.939 1.987
15 601 2145 205 866 396 1279 599 2096 421 1049 394 1230 0 0 95 495 746 973 0 67 0 3 1675 1624 .31 3.23 3.122 3.048 3.109 1.631 52 269 3.405 .376 90 4040 5320 47 56 287 296 0 1387 560 827 2.088 1355 795 .479 2.019 1.062 1.013
16 29347 32770 206 848 29141 31922 25827 30886 492 1041 25621 30038 1 0 11567 8995 988 1011 100 100 100 100 61063 55659 .913 1.095 1.172 1.124 1.121 1.153 52 305 1.063 .951 90 4180 5310 46 55 301 310 0 21189 548 20641 .708 19971 19423 1.412 .758 -.498 -.4
17 2626 12446 200 810 2426 11636 2756 13205 221 832 2556 12395 0 0 762 3856 211 282 98 100 96 100 14062 14951 .208 4.796 4.849 4.967 4.652 1.341 52 254 4.934 .929 80 4320 5310 47 55 316 324 0 8048 524 7524 3.101 8538 8015 .322 3.136 1.633 1.649
18 1631 1981 197 775 1434 1206 1640 1984 211 803 1443 1209 0 0 310 497 141 255 100 98 100 94 2640 2652 1.189 .841 .838 .789 .842 1.518 52 274 .934 .751 80 4470 5310 47 55 331 339 0 1281 501 780 .544 1283 782 1.839 .542 -.879 -.884
19 3055 5669 198 789 2857 4880 3086 6016 212 801 2888 5227 0 0 1281 1760 84 234 100 100 100 98 7737 8115 .585 1.708 1.81 1.724 1.732 1.343 52 286 1.673 .94 80 4620 5310 47 55 346 354 0 3666 510 3155 1.104 3890 3380 .905 1.17 .143 .227
20 9111 7860 203 817 8908 7043 9372 7764 226 825 9169 6947 0 0 2001 1435 87 229 100 100 100 100 15951 16116 1.265 .791 .758 .797 .793 1.157 32 214 .778 .967 70 4760 5310 47 54 360 367 0 5082 528 4554 .511 5020 4492 1.956 .49 -.968 -1.029

Total number of rows: 43200

Table truncated, full table size 9877 Kbytes.




Supplementary data files not provided
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