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Sample GSM89967 Query DataSets for GSM89967
Status Public on Dec 30, 2005
Title FT2046 Inner cortex
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 cortex total RNA
Organism Homo sapiens
Characteristics Normal kidney,inner cortex total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23316.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 GPL1282
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
1 731 954 346 434 385 520 663 792 400 559 317 358 0 0 345 496 577 880 30 23 1 0 905 675 .74 1.351 1.129 4.009 1.292 12.513 80 383 .895 .59 100 2410 8630 38 48 48 58 0 1149 523 627 1.627 954 431 .615 1.361 .702 .444
2 1035 913 357 401 678 512 1086 913 373 435 729 512 0 0 495 313 137 221 80 80 70 55 1190 1241 1.324 .755 .702 1.815 .683 3.507 80 317 .459 .58 100 2560 8630 38 48 63 73 0 1100 483 617 .91 1100 617 1.099 .846 -.136 -.241
3 2742 7552 362 398 2380 7154 2917 7648 393 464 2555 7250 0 0 1431 3342 207 334 88 100 87 100 9534 9805 .333 3.006 2.838 5.955 2.799 9.552 80 378 1.955 .78 110 2700 8620 36 47 76 87 0 9099 480 8619 3.622 9214 8735 .276 3.419 1.857 1.773
4 3758 5641 365 417 3393 5224 2169 2909 415 503 1804 2492 0 0 3845 6028 356 666 82 77 75 67 8617 4296 .65 1.54 1.381 3.212 1.271 6.367 80 326 1.401 .9 100 2850 8630 38 48 92 102 0 6796 502 6294 1.855 3505 3002 .539 1.664 .891 .735
5 871 1745 363 391 508 1354 677 1298 406 480 314 907 0 0 545 1240 346 657 48 63 28 35 1862 1221 .375 2.665 2.889 5.507 2.294 11.871 80 319 .943 .42 100 3000 8630 38 48 107 117 0 2102 471 1631 3.211 1564 1093 .311 3.48 1.683 1.799
6 434 517 351 387 83 130 380 433 389 709 29 46 0 0 213 434 245 3327 20 0 3 0 213 75 .638 1.566 1.586 5.537 1.101 15.786 80 330 .365 .11 100 3140 8630 38 48 121 131 0 623 466 157 1.887 522 55 .53 1.911 .916 .934
7 481 945 357 377 124 568 474 959 381 673 117 582 0 0 216 549 192 3297 40 1 11 0 692 699 .218 4.581 4.974 4.03 2.783 4.448 80 335 2.076 .18 100 3290 8630 38 48 136 146 0 1139 454 684 5.519 1155 701 .181 5.993 2.464 2.583
8 7255 7364 363 383 6892 6981 5643 5377 383 423 5280 4994 0 0 6079 5559 136 215 90 96 87 93 13873 10274 .987 1.013 .946 3.49 1.192 6.486 80 329 .686 .71 100 3430 8630 38 48 150 160 0 8872 461 8411 1.22 6478 6017 .819 1.14 .287 .188
9 1690 1973 368 410 1322 1563 1297 1380 384 440 929 970 0 0 1356 1419 129 209 78 92 71 77 2885 1899 .846 1.182 1.044 4.13 1.089 12.523 80 326 .868 .79 100 3580 8630 38 48 165 175 0 2377 494 1883 1.424 1663 1169 .702 1.258 .51 .331
10 720 1347 373 419 347 928 507 978 384 459 134 559 0 0 620 982 85 244 56 68 42 55 1275 693 .374 2.674 4.172 6.71 2.462 13.761 80 311 1.01 .55 100 3730 8630 38 48 180 190 0 1623 505 1118 3.222 1178 673 .31 5.026 1.688 2.329
11 6309 2240 371 406 5938 1834 6139 1863 413 505 5768 1457 0 0 5112 1379 502 871 82 68 73 43 7772 7225 3.238 .309 .253 1.152 .35 2.238 80 311 .206 .56 100 3870 8630 38 48 194 204 0 2699 489 2210 .372 2245 1755 2.687 .304 -1.426 -1.716
12 2422 1771 371 403 2051 1368 1372 1162 425 499 1001 759 0 0 2122 1335 524 867 66 47 48 31 3419 1760 1.499 .667 .758 2.898 .68 6.305 80 311 .447 .54 100 4020 8630 38 48 209 219 0 2134 486 1648 .804 1400 914 1.244 .914 -.315 -.13
13 1520 1345 362 397 1158 948 1055 983 377 421 693 586 0 0 1165 894 110 171 81 91 71 68 2106 1279 1.222 .819 .846 3.809 .801 12.278 80 298 .579 .67 100 4160 8630 38 48 223 233 0 1620 478 1142 .986 1184 706 1.014 1.019 -.02 .027
14 603 879 349 376 254 503 453 622 367 401 104 246 0 0 348 602 111 173 47 57 37 41 757 350 .505 1.98 2.365 4.816 1.752 10.688 80 287 .874 .58 100 4310 8630 38 48 238 248 0 1059 453 606 2.386 749 296 .419 2.85 1.255 1.511
15 11555 19563 346 377 11209 19186 6754 12337 382 411 6408 11960 0 0 11370 18804 341 216 81 93 80 89 30395 18368 .584 1.712 1.866 4.255 1.925 6.417 120 403 1.361 .81 120 4450 8620 36 48 251 263 0 23570 454 23116 2.062 14864 14410 .485 2.249 1.044 1.169
16 2871 5933 355 400 2516 5533 2998 6118 380 422 2643 5718 0 0 1917 3284 363 201 73 96 72 93 8049 8361 .455 2.199 2.163 8.92 2.267 18.715 80 299 1.398 .72 100 4600 8630 38 48 267 277 0 7148 482 6666 2.65 7371 6889 .377 2.607 1.406 1.382
17 638 1339 349 375 289 964 550 1034 358 398 201 659 0 0 280 929 94 144 68 82 53 68 1253 860 .3 3.336 3.279 6.304 3.031 9.51 80 297 2.077 .65 100 4750 8630 38 48 282 292 0 1613 452 1161 4.019 1246 794 .249 3.95 2.007 1.982
18 439 386 349 353 90 33 375 363 363 368 26 10 0 0 215 162 103 125 32 22 21 10 123 36 2.727 .367 .385 1.762 .84 1.901 80 287 .143 .16 100 4890 8630 38 48 296 306 0 465 425 40 .442 437 12 2.264 .463 -1.179 -1.11
19 4352 1919 357 350 3995 1569 3762 1632 375 397 3405 1282 0 0 3395 1225 120 286 91 86 88 70 5564 4687 2.546 .393 .377 1.992 .45 6.961 80 300 .294 .78 100 5040 8630 38 48 311 321 0 2312 422 1890 .473 1966 1545 2.113 .454 -1.08 -1.14
20 1402 696 358 391 1044 305 1335 666 366 414 977 275 0 0 805 287 97 181 83 63 78 32 1349 1252 3.423 .292 .281 .769 .343 1.031 80 286 .215 .2 100 5190 8630 38 48 326 336 0 839 471 367 .352 802 331 2.841 .339 -1.506 -1.56

Total number of rows: 43008

Table truncated, full table size 9590 Kbytes.




Supplementary data files not provided
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