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Sample GSM229026 Query DataSets for GSM229026
Status Public on Feb 24, 2012
Title shgc150|PR00242 Macaque
Sample type genomic
 
Channel 1
Source name Normal human male genomic DNA
Organism Homo sapiens
Characteristics Normal human male genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Macaque genomic DNA
Organism Macaca sp.
Characteristics Macaque genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Comparative genomics, aCGH cell line
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 Sep 12, 2007
Last update date Feb 24, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL5845
Series (1)
GSE9028 Extended Primate aCGH

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 1897 1350 166 206 1731 1144 1934 1294 175 234 1768 1088 0 0 433 474 69 167 100 99 100 99 2875 2856 1.513 .661 .615 .66 .66 .26 69 427 .72 .99 90 2440 6200 43 52 47 56 0 1265 193 1072 .619 1213 1020 1.615 .577 -.691 -.794
2 2504 2247 167 219 2337 2028 2312 2271 177 258 2145 2052 0 0 691 741 66 159 100 100 100 100 4365 4197 1.152 .868 .957 .88 .85 .31 51 367 .9 .99 80 2590 6210 45 53 63 71 0 2106 205 1901 .813 2128 1923 1.23 .897 -.298 -.158
3 2496 1812 166 219 2330 1593 2372 1680 173 248 2206 1461 0 0 781 755 63 141 100 100 100 100 3923 3667 1.463 .684 .662 .69 .68 .27 60 367 .73 .99 80 2730 6210 45 53 77 85 0 1698 205 1493 .641 1574 1369 1.561 .621 -.642 -.688
4 1967 1874 159 213 1808 1661 1913 1871 165 244 1754 1658 0 0 451 546 58 145 100 100 100 100 3469 3412 1.089 .919 .945 .92 .94 .23 60 362 .96 .99 80 2880 6210 45 53 92 100 0 1756 200 1557 .861 1753 1554 1.161 .886 -.216 -.175
5 1311 1102 155 233 1156 869 1333 1050 161 257 1178 817 0 0 341 353 57 152 100 100 100 95 2025 1995 1.33 .752 .694 .79 .68 .38 60 364 .85 .98 80 3010 6210 45 53 105 113 0 1033 218 814 .704 984 766 1.419 .65 -.505 -.622
6 2228 2502 164 234 2064 2268 2221 2451 166 260 2057 2217 0 0 635 849 56 159 100 100 100 100 4332 4274 .91 1.099 1.078 1.09 1.1 .32 44 400 1.12 .99 70 3180 6210 45 52 122 129 0 2345 219 2125 1.03 2297 2078 .971 1.01 .042 .014
7 1846 1463 164 242 1682 1221 1879 1451 169 272 1715 1209 0 0 482 472 62 161 100 99 99 99 2903 2924 1.378 .726 .705 .78 .68 .53 80 292 .81 .99 100 3320 6210 44 54 135 145 0 1371 227 1144 .68 1360 1133 1.47 .661 -.556 -.598
8 2100 1572 164 232 1936 1340 2021 1522 170 257 1857 1290 0 0 598 425 62 157 100 100 100 100 3276 3147 1.445 .692 .695 .72 .73 .27 69 305 .75 .99 90 3440 6210 44 53 147 156 0 1473 217 1256 .649 1426 1209 1.542 .651 -.624 -.619
9 1620 1848 167 225 1453 1623 1617 1809 173 245 1450 1584 0 0 310 532 56 141 100 100 100 100 3076 3034 .895 1.117 1.092 1.15 1.16 .43 80 289 1.15 .99 100 3590 6220 45 55 162 172 0 1732 211 1521 1.047 1695 1484 .955 1.024 .066 .034
10 2853 3272 164 222 2689 3050 2917 3438 166 244 2753 3216 0 0 696 849 58 141 100 100 100 100 5739 5969 .882 1.134 1.168 1.15 1.18 .27 86 280 1.15 .99 100 3730 6220 45 55 176 186 0 3066 208 2858 1.063 3222 3014 .941 1.095 .088 .131
11 1334 1426 159 218 1175 1208 1311 1419 164 231 1152 1201 0 0 224 390 63 131 100 100 100 100 2383 2353 .973 1.028 1.043 1.04 1.04 .34 70 350 1.07 .98 90 3880 6210 44 53 191 200 0 1336 204 1132 .963 1330 1126 1.038 .977 -.054 -.034
12 1641 1698 163 237 1478 1461 1714 1624 163 249 1551 1387 0 0 456 579 59 142 100 100 100 100 2939 2938 1.012 .988 .894 1.02 .93 .36 69 366 1.04 .99 90 4030 6220 45 54 206 215 0 1591 222 1369 .926 1522 1300 1.079 .838 -.11 -.255
13 2878 3806 167 248 2711 3558 2864 3768 174 262 2697 3520 0 0 515 802 67 146 100 100 100 100 6269 6217 .762 1.312 1.305 1.32 1.32 .27 69 362 1.33 .99 90 4170 6210 44 53 220 229 0 3567 232 3334 1.23 3531 3299 .813 1.223 .299 .291
14 2513 2860 171 231 2342 2629 2634 2921 178 257 2463 2690 0 0 628 834 63 147 100 100 100 100 4971 5153 .891 1.123 1.092 1.13 1.15 .3 80 314 1.14 .99 100 4340 6220 45 55 237 247 0 2680 216 2464 1.052 2737 2521 .951 1.024 .073 .034
15 1376 1516 156 223 1220 1293 1428 1525 163 245 1272 1302 0 0 378 468 54 145 100 100 99 97 2513 2574 .944 1.06 1.024 1.18 1.1 .84 69 341 1.11 .98 90 4470 6210 44 53 250 259 0 1421 209 1212 .993 1429 1220 1.007 .959 -.01 -.06
16 6193 7621 171 231 6022 7390 6140 7751 175 259 5969 7520 0 0 1351 1929 68 159 100 100 100 100 13412 13489 .815 1.227 1.26 1.21 1.28 .2 80 320 1.25 1 100 4640 6220 45 55 267 277 0 7142 216 6926 1.15 7264 7047 .87 1.181 .202 .24
17 2425 2599 183 254 2242 2345 2412 2565 189 279 2229 2311 0 0 369 521 74 158 100 100 100 100 4587 4540 .956 1.046 1.037 1.06 1.03 .28 70 310 1.08 .99 90 4780 6210 44 53 281 290 0 2436 238 2198 .98 2404 2166 1.02 .972 -.029 -.042
18 3148 4034 179 272 2969 3762 3176 4135 189 295 2997 3863 0 0 609 995 74 154 100 100 100 100 6731 6860 .789 1.267 1.289 1.27 1.3 .3 80 280 1.29 .99 100 4930 6220 45 55 296 306 0 3781 255 3526 1.187 3875 3620 .842 1.208 .248 .273
19 6924 7641 186 252 6738 7389 6741 7675 194 289 6555 7423 0 0 1311 1398 78 177 100 100 100 100 14127 13978 .912 1.097 1.132 1.1 1.12 .18 97 287 1.12 .99 110 5070 6210 43 54 309 320 0 7161 236 6925 1.028 7193 6957 .973 1.061 .039 .086
20 1759 1851 190 246 1569 1605 1779 1828 195 275 1589 1582 0 0 304 431 74 173 100 100 100 100 3174 3171 .978 1.023 .996 1.05 1.03 .34 86 287 1.06 .99 100 5220 6220 45 55 325 335 0 1735 231 1504 .959 1713 1483 1.043 .933 -.061 -.1

Total number of rows: 41472

Table truncated, full table size 9420 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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