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Sample GSM89940 Query DataSets for GSM89940
Status Public on Dec 30, 2005
Title FT2449 Papillary tips
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,papillary tips total RNA
Organism Homo sapiens
Characteristics Normal kidney,papillary tips total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/24863.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
1 819 814 122 115 697 699 718 581 127 118 596 466 0 0 673 720 48 37 70 80 68 75 1396 1062 .997 1.003 .782 .65 .801 3.217 80 353 1.055 .75 100 1690 8350 42 52 80 90 0 1131 160 971 1.393 807 647 .718 1.086 .478 .119
2 593 734 125 117 468 617 259 414 127 123 134 297 0 0 641 686 24 39 58 76 55 63 1085 431 .759 1.318 2.216 1.172 1.156 3.005 80 305 1.136 .84 100 1820 8330 40 50 93 103 0 1019 163 857 1.831 575 413 .546 3.078 .873 1.622
3 3053 9784 127 120 2926 9664 3829 11324 132 124 3702 11204 0 0 2194 6627 46 39 85 100 83 99 12590 14906 .303 3.303 3.026 3.49 3.148 3.098 120 510 3.634 .87 130 1970 8340 39 52 106 119 0 13589 167 13422 4.587 15728 15561 .218 4.203 2.198 2.072
4 7422 7222 128 124 7294 7098 2737 3783 130 129 2609 3659 0 0 8988 8352 27 34 85 95 80 92 14392 6268 1.028 .973 1.402 1.126 .998 4.125 80 311 .932 .83 110 2120 8350 41 52 122 133 0 10031 172 9858 1.352 5254 5082 .74 1.948 .435 .962
5 883 1314 129 123 754 1191 208 549 133 128 79 426 0 0 1109 1509 27 36 61 77 53 72 1945 505 .633 1.58 5.392 1.227 1.202 4.804 80 375 1.493 .83 110 2270 8330 39 50 137 148 0 1825 171 1654 2.194 763 592 .456 7.489 1.133 2.905
6 507 678 130 121 377 557 357 506 137 127 227 385 0 0 427 559 47 44 66 76 61 72 934 612 .677 1.477 1.696 1.118 1.057 3.409 80 385 1.471 .82 110 2410 8350 41 52 151 162 0 942 168 774 2.052 703 535 .487 2.356 1.037 1.236
7 431 497 127 122 304 375 340 385 129 126 213 263 0 0 356 387 24 39 67 80 62 73 679 476 .811 1.234 1.235 1.208 .968 2.707 80 309 1.178 .81 100 2560 8340 41 51 167 177 0 690 169 521 1.713 535 365 .584 1.715 .777 .778
8 4992 3955 124 118 4868 3837 441 946 128 122 317 828 0 0 7513 5098 32 38 76 87 63 76 8705 1145 1.269 .788 2.612 1.217 .757 5.343 120 401 .658 .83 120 2700 8340 40 52 180 192 0 5493 164 5329 1.095 1314 1150 .913 3.628 .131 1.859
9 1156 2200 126 115 1030 2085 206 559 129 120 80 444 0 0 1738 2995 29 36 65 84 55 75 3115 524 .494 2.024 5.55 1.712 1.532 4.292 120 397 2.033 .79 120 2850 8340 40 52 195 207 0 3056 160 2896 2.811 776 617 .356 7.708 1.491 2.946
10 752 1759 125 114 627 1645 513 1122 128 118 388 1008 0 0 675 1510 31 33 73 92 67 86 2272 1396 .381 2.624 2.598 2.196 2.127 4.178 52 217 2.688 .84 90 3000 8330 40 49 211 220 0 2443 158 2285 3.644 1558 1400 .274 3.608 1.865 1.851
11 6714 3699 126 118 6588 3581 5830 3539 129 121 5704 3421 0 0 6097 2876 30 37 87 96 81 90 10169 9125 1.84 .544 .6 .697 .483 4.982 156 617 .428 .77 140 3130 8340 39 53 222 236 0 5138 164 4974 .755 4915 4751 1.325 .833 -.406 -.264
12 3072 1417 135 128 2937 1289 2016 1084 137 131 1881 956 0 0 3069 1280 33 38 73 90 73 76 4226 2837 2.279 .439 .508 .375 .407 3.899 52 255 .366 .82 90 3300 8330 40 49 241 250 0 1968 178 1790 .61 1506 1328 1.641 .706 -.714 -.502
13 1403 1093 129 122 1274 971 465 775 131 125 336 653 0 0 1589 973 24 35 70 81 62 72 2245 989 1.312 .762 1.943 .889 .647 5.55 80 363 .565 .72 110 3440 8330 39 50 254 265 0 1518 169 1349 1.059 1076 907 .945 2.699 .082 1.433
14 549 342 129 126 420 216 386 312 131 129 257 186 0 0 462 213 24 36 73 71 70 61 636 443 1.944 .514 .724 .558 .513 4.714 80 342 .379 .68 110 3590 8340 40 51 269 280 0 475 175 300 .714 433 258 1.4 1.005 -.485 .007
15 5922 4279 126 123 5796 4156 1231 1515 127 129 1105 1392 0 0 7110 4618 24 37 89 98 85 93 9952 2497 1.395 .717 1.26 .868 .713 5.304 120 396 .587 .74 120 3720 8340 40 52 282 294 0 5943 171 5772 .996 2104 1933 1.004 1.75 -.006 .807
16 1922 2058 124 119 1798 1939 520 862 126 124 396 743 0 0 2350 2110 26 36 69 90 63 82 3737 1139 .927 1.078 1.876 1.439 .994 5.107 120 420 .934 .71 120 3860 8340 40 52 296 308 0 2858 165 2693 1.498 1197 1032 .668 2.606 .583 1.382
17 587 1484 137 127 450 1357 603 1591 138 129 466 1464 0 0 367 951 27 34 78 92 76 84 1807 1930 .332 3.016 3.142 1.801 2.531 3.653 52 310 3.737 .72 90 4030 8330 40 49 314 323 0 2061 176 1885 4.188 2210 2033 .239 4.363 2.066 2.125
18 384 250 141 130 243 120 344 236 144 132 203 106 0 0 258 124 27 34 73 69 63 57 363 309 2.025 .494 .522 .484 .507 2.7 52 192 .39 .58 80 4180 8330 41 49 330 338 0 347 181 167 .686 328 147 1.458 .725 -.544 -.463
19 3851 1361 139 129 3712 1232 4562 1476 143 132 4423 1347 0 0 2710 741 33 37 90 92 87 90 4944 5770 3.013 .332 .305 .51 .306 4.775 120 425 .226 .7 120 4290 8340 40 52 339 351 0 1890 179 1711 .461 2050 1871 2.169 .423 -1.117 -1.241
20 2388 1693 145 130 2243 1563 890 1029 151 134 745 899 0 0 2511 1551 47 39 72 90 67 82 3806 1644 1.435 .697 1.207 .762 .645 5.501 80 309 .586 .77 110 4460 8350 41 52 356 367 0 2351 181 2171 .968 1429 1249 1.033 1.676 -.047 .745

Total number of rows: 43008

Table truncated, full table size 9442 Kbytes.




Supplementary data files not provided
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