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Sample GSM89966 Query DataSets for GSM89966
Status Public on Dec 30, 2005
Title FT2449 Inner medulla
Sample type RNA
 
Channel 1
Source name Universal Human Reference total RNA
Organism Homo sapiens
Characteristics Universal Human Reference total RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Normal kidney,inner medulla total RNA
Organism Homo sapiens
Characteristics Normal kidney,inner medulla total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/24859.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 Dec 29, 2005
Last update date Sep 22, 2006
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 GPL3044
Series (1)
GSE3931 Gene expression in the normal adult human kidney

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
1 663 972 146 127 517 845 392 539 148 129 246 412 0 0 625 960 22 28 66 80 60 75 1362 658 .612 1.634 1.675 3.349 1.319 7.895 80 393 1.243 .79 100 1640 8390 46 56 75 85 0 1130 148 983 1.9 627 479 .526 1.947 .926 .962
2 627 771 150 128 477 643 288 277 151 135 138 149 0 0 591 878 27 39 68 68 60 60 1120 287 .742 1.348 1.08 4.189 1.12 12.415 120 421 1.025 .71 130 1790 8400 45 58 88 101 0 897 149 748 1.567 322 173 .638 1.255 .648 .328
3 3048 13051 158 133 2890 12918 3660 14944 160 143 3502 14811 0 0 2120 7969 34 49 85 100 84 99 15808 18313 .224 4.47 4.229 9.803 4.289 16.915 120 485 3.208 .77 130 1910 8390 44 57 100 113 0 15176 155 15021 5.198 17377 17222 .192 4.918 2.378 2.298
4 5288 8609 165 148 5123 8461 1126 4024 171 158 961 3876 0 0 7217 10306 38 52 72 95 63 87 13584 4837 .605 1.652 4.033 6.042 1.392 11.833 80 336 1.151 .77 100 2070 8390 46 56 118 128 0 10010 172 9838 1.92 4679 4507 .521 4.69 .941 2.23
5 1072 2290 159 138 913 2152 471 1616 162 142 312 1478 0 0 1159 2333 33 37 66 92 62 85 3065 1790 .424 2.357 4.737 6.812 1.947 15.303 80 338 1.541 .73 100 2220 8390 46 56 133 143 0 2663 160 2502 2.741 1879 1719 .365 5.508 1.455 2.462
6 570 649 159 136 411 513 438 454 160 138 279 318 0 0 453 524 28 33 72 80 70 71 924 597 .801 1.248 1.14 1.815 1.22 2.601 80 344 .953 .8 100 2370 8400 47 57 148 158 0 755 158 597 1.451 528 370 .689 1.325 .537 .406
7 471 971 155 136 316 835 341 703 156 138 186 567 0 0 400 806 25 31 62 83 60 82 1151 753 .378 2.642 3.048 6.025 2.144 14.418 80 345 1.566 .7 110 2510 8390 45 56 161 172 0 1129 158 971 3.073 817 659 .325 3.545 1.619 1.826
8 5367 6401 156 130 5211 6271 484 1020 157 133 328 890 0 0 7185 8595 26 32 74 88 63 82 11482 1218 .831 1.203 2.713 3.479 1.137 10.962 120 382 .954 .8 120 2660 8400 46 58 176 188 0 7443 151 7292 1.399 1186 1035 .715 3.155 .485 1.658
9 2247 3157 156 128 2091 3029 1638 2503 160 131 1482 2375 0 0 2161 2934 40 35 75 91 67 86 5120 3857 .69 1.449 1.603 6.515 1.367 16.014 80 356 1.042 .75 110 2810 8390 45 56 191 202 0 3671 149 3522 1.684 2910 2762 .594 1.863 .752 .898
10 813 1647 170 137 643 1510 551 1027 199 196 381 890 0 0 730 1529 166 276 56 62 53 59 2153 1271 .426 2.348 2.336 2.376 2.077 2.433 32 144 1.423 .66 70 2930 8390 47 54 205 212 0 1915 159 1756 2.731 1194 1035 .366 2.716 1.449 1.442
11 7408 3347 152 129 7256 3218 7865 3890 164 143 7713 3761 0 0 6287 2559 85 138 84 80 78 73 10474 11474 2.255 .443 .488 4.345 .409 11.924 156 624 .312 .74 140 3080 8390 44 58 217 231 0 3892 150 3742 .516 4523 4373 1.939 .567 -.955 -.819
12 2608 1838 150 125 2458 1713 1375 1153 153 128 1225 1028 0 0 2774 1830 27 27 77 88 71 83 4171 2253 1.435 .697 .839 4.835 .611 14.701 80 284 .519 .77 100 3250 8390 46 56 236 246 0 2137 145 1992 .81 1341 1195 1.234 .976 -.303 -.035
13 1639 1536 140 124 1499 1412 931 1030 141 128 791 906 0 0 1679 1378 27 30 68 87 68 85 2911 1697 1.062 .942 1.145 3.433 .836 12.279 80 322 .66 .77 110 3390 8390 45 56 249 260 0 1786 144 1642 1.095 1198 1053 .913 1.332 .131 .413
14 590 470 149 130 441 340 446 336 153 135 297 206 0 0 472 358 30 40 75 72 68 65 781 503 1.297 .771 .694 1.376 .66 2.229 80 284 .525 .68 100 3540 8400 47 57 265 275 0 547 151 395 .896 391 240 1.115 .807 -.158 -.31
15 5221 7518 142 126 5079 7392 1788 4009 146 130 1646 3883 0 0 6035 8043 30 37 81 95 79 93 12471 5529 .687 1.455 2.359 4.952 1.237 12.687 120 360 .993 .72 120 3680 8400 46 58 278 290 0 8742 147 8595 1.692 4662 4515 .591 2.743 .759 1.456
16 1924 3210 132 117 1792 3093 726 2030 134 119 594 1913 0 0 2170 3282 26 31 74 91 68 88 4885 2507 .579 1.726 3.221 5.541 1.385 13.196 120 360 1.222 .77 120 3830 8400 46 58 293 305 0 3733 136 3597 2.007 2360 2224 .498 3.745 1.005 1.905
17 430 1560 135 119 295 1441 306 1106 138 120 171 987 0 0 340 1281 27 31 63 91 61 90 1736 1158 .205 4.885 5.772 5.476 3.859 8.019 80 319 3.182 .76 100 3980 8390 46 56 309 319 0 1814 138 1676 5.68 1286 1148 .176 6.712 2.506 2.747
18 447 300 147 126 300 174 506 309 151 127 359 183 0 0 231 148 27 28 84 78 80 71 474 542 1.724 .58 .51 .704 .584 .562 52 222 .428 .68 90 4130 8400 47 56 324 333 0 349 147 202 .674 359 213 1.483 .593 -.568 -.755
19 3839 1936 142 126 3697 1810 4292 2008 145 127 4150 1882 0 0 2369 1175 28 29 97 97 94 95 5507 6032 2.043 .49 .453 2.658 .508 7.419 120 468 .375 .75 130 4250 8400 45 58 334 347 0 2251 147 2105 .569 2335 2188 1.757 .527 -.813 -.923
20 2227 1488 141 127 2086 1361 2214 958 145 129 2073 831 0 0 1930 1315 32 34 85 93 81 85 3447 2904 1.533 .652 .401 2.18 .643 4.973 80 285 .47 .7 110 4410 8410 47 58 351 362 0 1730 148 1583 .759 1114 966 1.318 .466 -.398 -1.101

Total number of rows: 43008

Table truncated, full table size 9640 Kbytes.




Supplementary data files not provided
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