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Sample GSM89947 Query DataSets for GSM89947
Status Public on Dec 30, 2005
Title FT2449 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 FT2449f-Normal kidney,pelvis total RNA
Organism Homo sapiens
Characteristics FT2449f-Normal kidney,pelvis total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/24866.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
1 591 427 115 97 476 330 465 349 121 103 350 252 0 0 434 354 74 92 76 57 65 53 806 602 1.442 .693 .72 .631 .7 3.058 80 460 .793 .92 110 1680 8960 46 57 62 73 0 593 135 458 .963 485 350 1.039 1 -.055 0
2 588 453 120 99 468 354 517 404 128 108 397 305 0 0 390 339 96 115 78 61 65 55 822 702 1.322 .756 .768 .707 .779 2.93 80 275 .835 .92 100 1810 8960 47 57 76 86 0 629 138 492 1.051 561 424 .952 1.067 .071 .094
3 2676 4718 115 96 2561 4622 3041 5470 119 100 2926 5374 0 0 1496 2643 30 33 97 98 95 95 7183 8300 .554 1.805 1.837 1.817 1.742 2.509 120 460 1.852 .94 130 1940 8960 45 58 87 100 0 6553 133 6419 2.507 7597 7464 .399 2.551 1.326 1.351
4 5719 4085 115 102 5604 3983 3435 2180 139 144 3320 2078 0 0 5856 4470 159 288 81 67 77 61 9587 5398 1.407 .711 .626 .634 .726 2.906 80 293 .735 .96 100 2100 8960 47 57 105 115 0 5674 142 5532 .987 3028 2886 1.013 .869 -.019 -.202
5 817 1187 116 93 701 1094 537 747 134 126 421 654 0 0 725 1153 142 257 71 58 58 52 1795 1075 .641 1.561 1.553 1.128 1.338 2.972 80 368 1.685 .89 110 2250 8960 46 57 119 130 0 1649 129 1519 2.168 1038 908 .461 2.158 1.116 1.109
6 477 427 118 99 359 328 341 390 124 105 223 291 0 0 362 294 40 55 73 73 65 65 687 514 1.095 .914 1.305 1.067 .888 3.129 80 365 .859 .88 100 2400 8960 47 57 135 145 0 593 138 456 1.269 542 404 .788 1.812 .344 .858
7 423 1174 115 102 308 1072 349 864 125 114 234 762 0 0 306 1008 65 72 66 82 62 73 1380 996 .287 3.481 3.256 2.644 3.37 2.75 80 348 3.584 .92 110 2550 8970 47 58 149 160 0 1631 142 1489 4.834 1200 1058 .207 4.523 2.273 2.177
8 5760 10684 118 91 5642 10593 4050 8331 124 105 3932 8240 0 0 5282 9564 50 59 87 95 86 88 16235 12172 .533 1.878 2.096 1.947 1.78 3.302 80 369 1.933 .92 110 2690 8960 46 57 163 174 0 14839 126 14713 2.608 11571 11444 .383 2.911 1.383 1.541
9 1937 1769 121 97 1816 1672 1600 1101 127 103 1479 1004 0 0 1713 1641 45 40 85 82 73 81 3488 2483 1.086 .921 .679 .749 .815 2.56 80 341 .941 .96 100 2840 8960 47 57 179 189 0 2457 135 2322 1.279 1529 1394 .782 .943 .355 -.085
10 805 921 129 104 676 817 914 784 160 137 785 680 0 0 593 643 147 148 62 81 62 65 1493 1465 .827 1.209 .866 1.417 1.308 2.104 32 154 1.015 .9 70 2970 8960 48 55 193 200 0 1279 144 1135 1.679 1089 944 .596 1.203 .747 .267
11 6762 2446 115 92 6647 2354 8257 2790 135 110 8142 2698 0 0 4055 1302 109 102 95 93 90 90 9001 10840 2.824 .354 .331 .424 .351 2.489 120 501 .322 .93 130 3110 8960 45 58 204 217 0 3397 128 3269 .492 3875 3747 2.033 .46 -1.024 -1.12
12 2198 1445 109 93 2089 1352 2062 928 111 97 1953 835 0 0 1887 1297 26 37 91 87 87 80 3441 2788 1.545 .647 .428 .595 .707 2.931 80 283 .657 .96 100 3270 8960 47 57 222 232 0 2007 129 1878 .899 1289 1160 1.112 .594 -.154 -.752
13 1481 1022 105 87 1376 935 1429 866 111 91 1324 779 0 0 1120 831 28 38 83 86 80 81 2311 2103 1.472 .68 .588 .673 .69 2.279 80 281 .706 .96 100 3420 8960 47 57 237 247 0 1419 121 1299 .944 1203 1082 1.06 .817 -.084 -.291
14 539 337 119 98 420 239 516 263 125 109 397 165 0 0 361 229 42 54 82 73 72 58 659 562 1.757 .569 .416 .53 .546 2.28 80 301 .59 .89 100 3560 8970 48 58 251 261 0 468 136 332 .79 365 229 1.265 .577 -.339 -.793
15 6677 5589 119 103 6558 5486 6700 4632 287 263 6581 4529 0 0 4912 4845 1572 1106 75 67 67 57 12044 11110 1.195 .837 .688 .769 .895 4.228 80 342 .905 .94 110 3710 8960 46 57 265 276 0 7763 143 7619 1.162 6433 6290 .861 .956 .216 -.065
16 1872 2318 117 92 1755 2226 1280 1098 143 106 1163 1006 0 0 1826 2487 275 99 58 74 54 67 3981 2169 .788 1.268 .865 1.222 1.408 3.045 120 366 1.352 .94 120 3850 8970 47 59 279 291 0 3219 128 3092 1.762 1525 1397 .568 1.201 .817 .265
17 449 999 112 92 337 907 478 1008 113 97 366 916 0 0 274 720 28 32 86 90 80 81 1244 1282 .372 2.691 2.503 2.2 2.619 2.552 80 306 2.797 .94 100 4000 8960 47 57 295 305 0 1388 128 1260 3.738 1400 1272 .268 3.476 1.902 1.797
18 408 219 105 93 303 126 393 212 129 110 288 119 0 0 209 108 141 127 75 48 50 15 429 407 2.405 .416 .413 .369 .38 1.776 52 186 .386 .77 80 4150 8960 48 56 311 319 0 304 129 175 .578 294 165 1.731 .574 -.792 -.801
19 2920 1388 105 87 2815 1301 3445 1569 121 101 3340 1482 0 0 1601 710 99 95 93 93 89 90 4116 4822 2.164 .462 .444 .519 .464 2.38 120 416 .446 .96 120 4270 8960 46 58 321 333 0 1928 121 1807 .642 2179 2058 1.558 .616 -.64 -.698
20 1356 764 112 92 1244 672 1060 673 119 102 948 581 0 0 1010 541 42 54 87 83 85 78 1916 1529 1.851 .54 .613 .497 .519 3.427 80 259 .518 .93 100 4430 8970 48 58 338 348 0 1061 128 933 .75 935 807 1.333 .851 -.415 -.232

Total number of rows: 43008

Table truncated, full table size 9348 Kbytes.




Supplementary data files not provided
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