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Sample GSM39967 Query DataSets for GSM39967
Status Public on Feb 21, 2005
Title Muscle, abdominal 0031
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Muscle, abdominal 0031
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-03/14631.gif
 
Submission date Jan 26, 2005
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 GPL1825
Series (1)
GSE2193 Normal_human_tissues

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 1270 1437 218 224 1052 1213 1316 1402 238 242 1098 1178 0 0 336 454 121 120 100 100 100 98 2265 2276 .867 1.153 1.073 1.128 1.143 1.425 52 233 1.118 .9 80 1230 8290 69 77 67 75 -100 1198 187 1011 .961 1168 982 1.041 .894 -.162 -.058
2 1227 1114 245 231 982 883 1381 1298 371 331 1136 1067 0 0 813 575 481 401 66 75 58 75 1865 2203 1.112 .899 .939 1.164 .879 3.124 12 93 1.084 .88 50 1380 8270 68 73 83 88 -100 928 193 736 .749 1082 889 1.335 .783 -.353 -.416
3 6354 7157 225 241 6129 6916 7134 7684 271 283 6909 7443 0 0 2550 2569 281 238 96 98 95 98 13045 14352 .886 1.128 1.077 1.242 1.105 1.554 80 297 1.106 .96 100 1510 8280 67 77 94 104 0 5964 201 5763 .94 6403 6203 1.063 .898 -.089 -.156 -.089
4 1755 2079 227 239 1528 1840 1999 2013 253 276 1772 1774 0 0 699 646 192 168 100 100 100 100 3368 3546 .83 1.204 1.001 1.285 1.261 1.535 12 62 1.162 .92 50 1650 8290 70 75 110 115 -100 1733 199 1533 1.003 1678 1478 .997 .834 -.261 .005
5 1795 1495 215 244 1580 1251 1872 1498 246 271 1657 1254 0 0 596 410 212 159 96 98 94 98 2831 2911 1.263 .792 .757 .856 .813 1.667 52 244 .726 .92 90 1770 8270 66 75 120 129 -100 1246 203 1043 .66 1248 1045 1.516 .631 -.665 -.6
6 1058 1332 221 244 837 1088 875 992 227 257 654 748 0 0 728 789 55 102 100 91 91 83 1925 1402 .769 1.3 1.144 1.24 1.334 2.663 12 68 1.64 .87 50 1920 8290 70 75 137 142 -100 1110 203 907 1.083 827 623 .923 .953 -.069 .115
7 1597 1397 229 239 1368 1158 1644 1348 254 307 1415 1109 0 0 329 339 147 270 100 100 100 96 2526 2524 1.181 .846 .784 .835 .892 1.391 52 193 .872 .86 90 2040 8290 68 77 147 156 0 1164 199 965 .705 1123 924 1.418 .653 -.503 -.615 -.503
8 2467 3526 233 237 2234 3289 2352 3145 326 410 2119 2908 0 0 598 1170 285 458 100 100 100 100 5523 5027 .679 1.472 1.372 1.44 1.418 1.292 52 156 1.513 .91 90 2180 8280 67 76 161 170 -100 2938 198 2741 1.227 2621 2423 .815 1.144 .194 .295
9 520 526 224 229 296 297 340 380 259 300 116 151 0 0 457 445 190 298 46 27 25 17 593 267 .997 1.003 1.302 1.183 1.119 3.027 80 290 1.183 .84 100 2280 8250 64 74 171 181 -50 438 191 248 .836 317 126 1.196 1.085 .117 -.258
10 747 1032 218 230 529 802 764 975 223 246 546 745 0 0 301 442 50 115 92 98 87 95 1331 1291 .66 1.516 1.364 1.717 1.522 2.13 80 257 1.572 .89 100 2440 8260 65 75 187 197 0 860 192 668 1.263 813 621 .792 1.137 .337 .185 .337
11 3175 1270 211 231 2964 1039 3516 1329 216 239 3305 1098 0 0 1281 641 51 87 100 93 100 88 4003 4403 2.853 .351 .332 .29 .35 2.211 80 264 .354 .89 100 2570 8250 64 74 200 210 0 1058 193 866 .292 1108 915 3.423 .277 -1.775 -1.853 -1.775
12 1687 3531 224 245 1463 3286 1698 3555 235 257 1474 3310 0 0 222 662 65 96 100 100 100 100 4749 4784 .445 2.246 2.246 2.225 2.29 1.228 32 165 2.337 .96 70 2700 8250 65 72 214 221 0 2943 204 2738 1.872 2963 2758 .534 1.871 .904 .904 .904
13 1195 2567 223 242 972 2325 1191 2513 230 256 968 2271 0 0 270 752 57 98 100 100 100 100 3297 3239 .418 2.392 2.346 2.35 2.312 1.321 52 243 2.522 .94 90 2840 8260 65 74 227 236 0 2139 202 1938 1.993 2094 1893 .502 1.955 .995 .967 .995
14 1531 3925 238 259 1293 3666 1596 4021 245 281 1358 3762 0 0 421 977 54 104 100 100 100 100 4959 5120 .353 2.835 2.77 2.931 2.743 1.393 52 212 2.824 .93 80 2980 8260 66 74 242 250 0 3271 216 3055 2.363 3351 3135 .423 2.309 1.24 1.207 1.24
15 1737 4603 248 267 1489 4336 1786 4720 249 282 1538 4453 0 0 549 1294 51 103 100 100 100 100 5825 5991 .343 2.912 2.895 3.005 2.962 1.232 32 162 2.873 .96 70 3120 8240 64 71 256 263 0 3836 223 3613 2.427 3933 3711 .412 2.413 1.279 1.271 1.279
16 2604 8816 239 267 2365 8549 2719 8999 245 276 2480 8732 0 0 538 1493 54 95 100 100 100 100 10914 11212 .277 3.615 3.521 3.668 3.538 1.219 80 357 3.636 .96 110 3240 8250 63 74 266 277 0 7347 223 7124 3.012 7499 7277 .332 2.934 1.591 1.553 1.591
17 1101 1083 233 264 868 819 1162 1033 238 270 929 769 0 0 237 436 51 93 100 100 100 100 1687 1698 1.06 .944 .828 .858 .983 1.599 52 236 1.096 .86 90 3370 8250 64 73 280 289 0 903 220 683 .786 861 641 1.272 .69 -.347 -.536 -.347
18 758 427 229 264 529 163 736 413 233 274 507 149 0 0 254 165 49 93 100 71 100 32 692 656 3.245 .308 .294 .317 .33 2.096 80 265 .333 .6 100 3520 8250 64 74 295 305 0 356 220 136 .257 344 124 3.894 .245 -1.961 -2.03 -1.961
19 741 8170 234 272 507 7898 730 8804 240 278 496 8532 0 0 265 1893 51 88 97 100 93 100 8405 9028 .064 15.578 17.202 16.863 16.285 1.537 80 227 15.718 .87 100 3640 8260 65 75 307 317 0 6808 227 6582 12.982 7337 7110 .077 14.335 3.698 3.841 3.698
20 2546 2237 235 274 2311 1963 2767 2377 239 279 2532 2103 0 0 803 650 49 85 100 100 100 97 4274 4635 1.177 .849 .831 .872 .839 1.424 80 294 .835 .95 110 3780 8270 65 76 320 331 0 1864 228 1636 .708 1981 1753 1.413 .692 -.498 -.531 -.498

Total number of rows: 44160

Table truncated, full table size 9903 Kbytes.




Supplementary data files not provided
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