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Sample GSM89954 Query DataSets for GSM89954
Status Public on Dec 30, 2005
Title FT2202 Glomeruli
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,glomeruli-2 total RNA
Organism Homo sapiens
Characteristics Normal kidney,glomeruli-2 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25599.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 GPL3275
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
1 370 435 86 107 284 328 396 452 86 111 310 345 0 0 165 167 14 31 93 93 93 93 612 655 .866 1.155 1.113 1.257 1.163 2.322 80 417 1.129 .8 100 1740 8590 66 76 45 55 0 870 214 656 2.31 904 690 .433 2.226 1.208 1.154
2 319 220 86 103 233 117 344 230 87 107 258 127 0 0 99 69 13 29 97 86 96 80 350 385 1.991 .502 .492 .51 .543 2.85 80 347 .47 .64 110 1890 8600 66 77 59 70 0 440 206 234 1.004 460 254 .996 .984 .006 -.023
3 1098 1897 86 105 1012 1792 1263 1981 87 108 1177 1876 0 0 453 559 14 28 99 100 99 100 2804 3053 .565 1.771 1.594 2.097 1.611 2.572 120 485 1.818 .82 130 2030 8590 64 77 72 85 0 3794 210 3584 3.542 3962 3752 .282 3.188 1.824 1.673
4 2439 665 88 108 2351 557 1547 294 90 110 1459 186 0 0 1965 615 15 28 100 84 98 80 2908 1645 4.221 .237 .127 .184 .242 3.838 52 250 .22 .77 90 2190 8600 67 76 90 99 0 1330 216 1114 .474 588 372 2.11 .255 -1.078 -1.972
5 410 499 88 110 322 389 451 516 89 111 363 406 0 0 160 163 14 30 95 96 95 96 711 769 .828 1.208 1.118 1.134 1.162 2.399 80 390 1.174 .74 110 2330 8590 65 76 103 114 0 998 220 778 2.416 1032 812 .414 2.237 1.273 1.162
6 269 306 89 109 180 197 282 316 90 112 193 207 0 0 80 102 15 31 96 92 94 86 377 400 .914 1.094 1.073 1.142 1.077 2.72 52 279 1.225 .7 90 2470 8590 66 75 118 127 0 612 218 394 2.189 632 414 .457 2.145 1.13 1.101
7 236 1701 87 105 149 1596 259 1874 89 107 172 1769 0 0 101 806 14 31 85 100 80 98 1745 1941 .093 10.711 10.285 9.558 10.149 1.768 80 332 11.587 .81 100 2610 8590 66 76 132 142 0 3402 210 3192 21.423 3748 3538 .047 20.57 4.421 4.362
8 3670 1419 85 105 3585 1314 3535 1323 87 106 3450 1218 0 0 2944 1086 14 30 98 85 96 82 4899 4668 2.728 .367 .353 .435 .397 4.906 120 474 .321 .84 120 2770 8600 66 78 147 159 0 2838 210 2628 .733 2646 2436 1.364 .706 -.448 -.502
9 790 421 87 103 703 318 787 429 88 106 700 326 0 0 395 203 14 27 100 98 98 86 1021 1026 2.211 .452 .466 .431 .478 2.462 52 257 .413 .8 80 2930 8600 68 76 165 173 0 842 206 636 .905 858 652 1.105 .931 -.144 -.102
10 193 345 84 101 109 244 155 327 86 105 71 226 0 0 102 147 16 28 81 93 68 93 353 297 .447 2.239 3.183 3.138 3.474 2.768 32 154 2.816 .5 70 3060 8590 67 74 178 185 0 690 202 488 4.477 654 452 .223 6.366 2.163 2.67
11 1738 514 85 107 1653 407 1926 511 87 109 1841 404 0 0 781 202 15 30 99 95 99 93 2060 2245 4.061 .246 .219 .265 .257 2.812 120 466 .205 .81 120 3190 8600 66 78 189 201 0 1028 214 814 .492 1022 808 2.031 .439 -1.022 -1.188
12 640 314 87 105 553 209 398 204 88 109 311 99 0 0 544 211 16 32 92 76 86 63 762 410 2.646 .378 .318 .358 .343 3.269 52 230 .322 .79 80 3340 8590 67 75 206 214 0 628 210 418 .756 408 198 1.323 .637 -.404 -.651
13 556 311 86 103 470 208 521 312 87 105 435 209 0 0 370 163 14 31 96 85 91 73 678 644 2.26 .443 .48 .496 .457 3.998 80 339 .355 .72 100 3490 8600 67 77 220 230 0 622 206 416 .885 624 418 1.13 .961 -.176 -.058
14 265 254 87 105 178 149 272 261 88 106 185 156 0 0 117 85 16 31 90 87 87 81 327 341 1.195 .837 .843 .969 .871 2.5 32 193 .756 .67 70 3630 8590 67 74 235 242 0 508 210 298 1.674 522 312 .597 1.686 .743 .754
15 2626 1965 83 104 2543 1861 2696 1887 84 104 2613 1783 0 0 1243 1008 15 31 97 100 97 100 4404 4396 1.366 .732 .682 .802 .76 3.087 80 446 .707 .83 110 3780 8600 66 77 248 259 0 3930 208 3722 1.464 3774 3566 .683 1.365 .55 .449
16 1134 1095 85 106 1049 989 1190 1047 85 107 1105 941 0 0 719 745 14 30 92 90 90 82 2038 2046 1.061 .943 .852 .868 .996 2.715 80 357 1.005 .86 100 3920 8610 68 78 263 273 0 2190 212 1978 1.886 2094 1882 .53 1.703 .915 .768
17 268 222 86 110 182 112 274 231 86 110 188 121 0 0 72 62 13 29 96 88 92 78 294 309 1.625 .615 .644 .572 .649 2.308 52 313 .603 .7 90 4070 8600 67 76 278 287 0 444 220 224 1.231 462 242 .813 1.287 .3 .364
18 224 194 87 105 137 89 238 191 88 106 151 86 0 0 81 60 13 29 92 86 92 73 226 237 1.539 .65 .57 .723 .679 2.545 52 289 .507 .45 90 4220 8600 67 76 293 302 0 388 210 178 1.299 382 172 .77 1.139 .378 .188
19 769 254 88 105 681 149 844 255 89 107 756 150 0 0 239 90 14 30 95 90 95 82 830 906 4.57 .219 .198 .171 .213 2.424 80 402 .178 .65 110 4360 8610 67 78 306 317 0 508 210 298 .438 510 300 2.285 .397 -1.192 -1.333
20 510 226 87 106 423 120 515 204 87 108 428 98 0 0 254 103 14 31 96 80 93 67 543 526 3.525 .284 .229 .264 .269 2.7 80 323 .25 .67 100 4520 8610 68 78 323 333 0 452 212 240 .567 408 196 1.763 .458 -.818 -1.127

Total number of rows: 43008

Table truncated, full table size 9140 Kbytes.




Supplementary data files not provided
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