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Sample GSM89956 Query DataSets for GSM89956
Status Public on Dec 30, 2005
Title FT2046 Pelvis
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,pelvis total RNA
Organism Homo sapiens
Characteristics Normal kidney,pelvis total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23329.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
1 857 756 291 349 566 407 888 673 298 382 597 324 0 0 499 403 75 190 75 66 67 43 973 921 1.391 .719 .543 2.299 .76 4.794 80 465 .556 .65 110 2380 8700 36 47 52 63 0 1350 623 727 1.284 1202 579 .779 .969 .361 -.045
2 953 892 308 354 645 538 1047 880 314 381 739 526 0 0 480 405 79 183 81 81 73 62 1183 1265 1.199 .834 .712 2.065 .734 4.343 80 362 .573 .62 110 2530 8700 36 47 67 78 0 1593 632 961 1.489 1571 939 .671 1.271 .575 .346
3 3232 4530 329 354 2903 4176 3760 4516 346 381 3431 4162 0 0 1690 2299 91 174 88 100 87 97 7079 7593 .695 1.439 1.213 6.066 1.392 16.143 80 357 1.192 .87 110 2670 8700 36 47 81 92 0 8089 632 7457 2.569 8064 7432 .389 2.166 1.361 1.115
4 6911 1372 333 370 6578 1002 3672 1120 344 386 3339 750 0 0 6932 1040 83 173 91 78 88 65 7580 4089 6.565 .152 .225 .654 .191 1.933 80 370 .129 .84 110 2820 8700 36 47 96 107 0 2450 661 1789 .272 2000 1339 3.676 .401 -1.878 -1.318
5 922 844 289 340 633 504 745 714 297 363 456 374 0 0 638 504 71 174 80 70 71 51 1137 830 1.256 .796 .82 1.32 .648 2.309 80 358 .622 .72 110 2970 8700 36 47 111 122 0 1507 607 900 1.422 1275 668 .703 1.465 .508 .551
6 447 502 280 326 167 176 382 479 284 353 102 153 0 0 202 232 60 179 60 45 46 22 343 255 .949 1.054 1.5 3.943 1.481 7.752 80 364 .534 .35 110 3110 8700 36 47 125 136 0 896 582 314 1.882 855 273 .531 2.679 .912 1.421
7 507 1136 291 346 216 790 489 1127 1156 1567 198 781 0 0 206 584 5733 7578 0 0 0 0 1006 979 .273 3.657 3.944 8.423 3.419 14.63 80 372 1.096 .45 110 3260 8700 36 47 140 151 0 2029 618 1411 6.531 2013 1395 .153 7.044 2.707 2.816
8 8174 6356 301 330 7873 6026 7111 7213 308 352 6810 6883 0 0 6679 4393 90 166 82 95 77 86 13899 13693 1.307 .765 1.011 3.912 .686 12.329 80 364 .607 .85 110 3400 8700 36 47 154 165 0 11350 589 10761 1.367 12880 12291 .732 1.805 .451 .852
9 2053 1152 306 340 1747 812 1660 994 320 389 1354 654 0 0 1574 694 103 361 83 62 75 45 2559 2008 2.151 .465 .483 1.869 .542 6.078 80 372 .38 .81 110 3550 8700 36 47 169 180 0 2057 607 1450 .83 1775 1168 1.205 .863 -.269 -.213
10 537 985 273 313 264 672 343 694 283 377 70 381 0 0 381 728 98 370 47 50 37 32 936 451 .393 2.545 5.443 4.888 2.482 7.009 80 356 1.372 .65 110 3700 8700 36 47 184 195 0 1759 559 1200 4.545 1239 680 .22 9.719 2.184 3.281
11 5788 1523 266 348 5522 1175 4355 1305 274 358 4089 957 0 0 4934 942 82 189 90 77 86 76 6697 5046 4.7 .213 .234 .932 .244 1.815 80 356 .151 .74 110 3840 8700 36 47 198 209 0 2720 621 2098 .38 2330 1709 2.632 .418 -1.396 -1.259
12 2127 911 263 335 1864 576 1203 802 266 347 940 467 0 0 1841 595 64 166 85 62 83 56 2440 1407 3.236 .309 .497 .843 .315 1.567 80 346 .233 .7 110 3990 8700 36 47 213 224 0 1627 598 1029 .552 1432 834 1.812 .887 -.858 -.173
13 1437 937 255 316 1182 621 968 773 263 341 713 457 0 0 1085 558 60 161 87 75 80 60 1803 1170 1.903 .525 .641 1.106 .51 1.807 80 323 .406 .75 110 4130 8700 36 47 227 238 0 1673 564 1109 .938 1380 816 1.066 1.145 -.092 .195
14 544 458 288 327 256 131 414 414 297 355 126 87 0 0 326 277 67 176 61 36 48 20 387 213 1.954 .512 .69 2.982 1.236 6.893 80 354 .385 .38 110 4280 8700 36 47 242 253 0 818 584 234 .914 739 155 1.094 1.233 -.13 .302
15 15527 10753 321 348 15206 10405 18622 12269 328 377 18301 11921 0 0 7762 4593 89 181 97 98 97 98 25611 30222 1.461 .684 .651 2.99 .68 10.126 80 356 .587 .89 110 4430 8700 36 47 257 268 0 19202 621 18580 1.222 21909 21288 .818 1.163 .289 .218
16 3180 3614 319 354 2861 3260 3397 3907 324 377 3078 3553 0 0 1964 1493 91 167 90 98 83 97 6121 6631 .878 1.139 1.154 5.428 1.157 13.422 80 350 .849 .85 110 4570 8700 36 47 271 282 0 6454 632 5821 2.035 6977 6345 .491 2.061 1.025 1.044
17 670 618 325 324 345 294 542 582 324 356 217 258 0 0 356 320 65 165 66 56 58 37 639 475 1.173 .852 1.189 3.667 .761 12.259 80 342 .547 .53 110 4720 8700 36 47 286 297 0 1104 579 525 1.522 1039 461 .657 2.123 .606 1.086
18 467 454 327 334 140 120 416 448 329 357 89 114 0 0 198 202 63 166 53 40 38 17 260 203 1.167 .857 1.281 3.931 1.057 9.85 80 336 .258 .19 110 4860 8700 36 47 300 311 0 811 596 214 1.531 800 204 .653 2.287 .614 1.194
19 2981 857 326 331 2655 526 2767 862 329 350 2441 531 0 0 2121 443 66 168 90 78 87 61 3181 2972 5.048 .198 .218 .734 .203 1.738 80 365 .137 .62 110 5010 8700 36 47 315 326 0 1530 591 939 .354 1539 948 2.827 .388 -1.499 -1.364
20 1284 675 331 333 953 342 1087 614 337 366 756 281 0 0 811 324 95 197 78 61 75 36 1295 1037 2.787 .359 .372 2.664 .439 11.314 80 355 .261 .59 110 5160 8700 36 47 330 341 0 1205 595 611 .641 1096 502 1.56 .664 -.642 -.591

Total number of rows: 43008

Table truncated, full table size 9538 Kbytes.




Supplementary data files not provided
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