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Sample GSM39927 Query DataSets for GSM39927
Status Public on Feb 21, 2005
Title Seminal vesicle 0234
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Seminal vesicle 0234
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/35856.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1824
Series (1)
GSE2193 Normal_human_tissues

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 594 568 177 145 417 423 614 583 181 149 437 438 0 0 223 206 43 44 98 94 90 94 840 875 .986 1.014 1.002 .998 .993 2.835 52 338 1.013 .78 90 1630 9220 53 62 38 47 0 304 78 226 .542 312 234 1.843 .536 -.882 -.9 -.882
2 554 527 184 149 370 378 594 575 185 152 410 426 0 0 152 191 45 43 94 90 94 88 748 836 .979 1.022 1.039 .884 1.101 2.577 52 303 1.088 .77 90 1780 9220 53 62 53 62 0 282 80 202 .546 307 228 1.83 .556 -.872 -.848 -.872
3 1439 5884 191 157 1248 5727 1538 6270 200 204 1347 6113 0 0 475 1678 64 216 98 100 97 100 6975 7460 .218 4.589 4.538 4.987 4.827 1.79 80 377 4.697 .9 100 1920 9230 54 64 67 77 0 3147 84 3063 2.454 3353 3269 .408 2.427 1.295 1.279 1.295
4 3130 26083 195 164 2935 25919 3224 27231 205 223 3029 27067 0 0 1443 12208 71 240 100 100 100 100 28854 30096 .113 8.831 8.936 8.68 8.395 1.952 52 320 10.056 .87 90 2060 9230 54 63 81 90 0 13948 88 13860 4.722 14562 14474 .212 4.779 2.24 2.257 2.24
5 629 1956 186 154 443 1802 698 2240 195 171 512 2086 0 0 250 802 70 92 85 100 83 97 2245 2598 .246 4.068 4.074 3.641 3.773 2.131 80 386 4.588 .81 100 2220 9230 54 64 97 107 0 1046 82 964 2.175 1198 1116 .46 2.179 1.121 1.123 1.121
6 601 465 189 144 412 321 627 472 188 151 438 328 0 0 168 103 45 50 96 100 96 98 733 766 1.283 .779 .749 .759 .732 1.557 52 275 .691 .8 90 2360 9230 54 63 111 120 0 249 77 172 .417 252 175 2.4 .4 -1.263 -1.32 -1.263
7 807 1413 189 143 618 1270 887 1580 190 144 698 1437 0 0 272 540 43 43 96 100 92 98 1888 2135 .487 2.055 2.059 2.128 1.961 2.317 80 357 2.238 .85 100 2510 9230 54 64 126 136 0 756 76 679 1.099 845 768 .91 1.101 .136 .139 .136
8 4061 19619 187 148 3874 19471 4585 20983 195 170 4398 20835 0 0 1397 7151 66 191 100 100 100 100 23345 25233 .199 5.026 4.737 5.078 5.035 1.777 80 390 5.566 .89 110 2660 9230 53 64 140 151 0 10491 79 10412 2.688 11221 11142 .372 2.533 1.426 1.341 1.426
9 972 2671 202 156 770 2515 1148 2701 214 191 946 2545 0 0 476 1312 82 238 86 96 76 90 3285 3491 .306 3.266 2.69 3.081 3.059 2.25 52 244 3.462 .84 80 2790 9240 56 64 155 163 0 1428 83 1345 1.747 1444 1361 .573 1.439 .805 .525 .805
10 360 397 206 156 154 241 298 334 208 166 92 178 0 0 195 199 55 52 59 78 48 67 395 270 .639 1.565 1.935 1.253 1.267 2.558 52 276 1.25 .78 80 2950 9230 55 63 171 179 -50 212 83 129 .837 179 95 1.195 1.035 .049 -.257
11 1805 3437 199 161 1606 3276 2020 3805 205 166 1821 3644 0 0 623 1120 54 49 97 100 96 100 4882 5465 .49 2.04 2.001 2.268 2.04 1.872 80 425 2.056 .91 110 3100 9230 53 64 184 195 0 1838 86 1752 1.091 2035 1949 .917 1.07 .125 .098 .125
12 1055 2113 211 168 844 1945 998 1991 245 221 787 1823 0 0 489 1385 169 271 90 87 84 78 2789 2610 .434 2.305 2.316 1.875 2.226 2.147 32 196 2.526 .91 70 3220 9230 55 62 198 205 0 1130 90 1040 1.232 1065 975 .811 1.239 .301 .309 .301
13 830 1747 194 162 636 1585 943 1871 219 196 749 1709 0 0 355 709 136 215 86 98 78 90 2221 2458 .401 2.492 2.282 2.81 2.441 2.415 52 322 2.484 .89 90 3380 9240 55 64 213 222 0 934 87 848 1.333 1001 914 .75 1.22 .414 .287 .414
14 365 5031 187 163 178 4868 315 4474 197 174 128 4311 0 0 169 3795 61 69 67 98 50 96 5046 4439 .037 27.348 33.68 20.478 22.854 2.434 52 303 26.635 .84 90 3530 9240 55 64 228 237 0 2690 87 2603 14.625 2393 2305 .068 18.011 3.87 4.171 3.87
15 3187 14424 188 152 2999 14272 3284 15743 191 158 3096 15591 0 0 1825 8067 42 44 97 100 95 100 17271 18687 .21 4.759 5.036 4.295 4.607 3.298 80 347 5.296 .85 100 3680 9230 54 64 243 253 0 7713 81 7632 2.545 8419 8337 .393 2.693 1.348 1.429 1.348
16 1491 6585 185 159 1306 6426 1594 7279 191 163 1409 7120 0 0 760 3257 55 46 90 100 87 100 7732 8529 .203 4.92 5.053 4.844 4.68 2.82 80 371 5.384 .86 100 3820 9230 54 64 257 267 0 3521 85 3436 2.631 3893 3807 .38 2.702 1.396 1.434 1.396
17 499 304 188 167 311 137 566 299 203 175 378 132 0 0 191 107 70 53 81 75 81 62 448 510 2.27 .441 .349 .495 .441 2.478 32 161 .361 .62 60 3990 9230 56 62 276 282 0 163 89 73 .236 160 71 4.245 .187 -2.086 -2.421 -2.086
18 531 195 191 168 340 27 596 204 201 176 405 36 0 0 229 60 58 58 81 37 78 3 367 441 12.593 .079 .089 .161 .149 1.88 32 166 .084 .26 60 4120 9230 56 62 289 295 0 104 90 14 .042 109 19 23.548 .048 -4.558 -4.395 -4.558
19 1045 2336 187 166 858 2170 1147 2485 198 174 960 2319 0 0 367 745 90 74 100 100 96 100 3028 3279 .395 2.529 2.416 2.677 2.651 1.82 80 487 2.611 .86 110 4270 9230 53 64 301 312 0 1249 89 1160 1.352 1329 1240 .739 1.292 .436 .369 .436
20 554 314 211 195 343 119 590 318 244 201 379 123 0 0 169 78 123 56 91 83 91 66 462 502 2.882 .347 .325 .309 .313 2.097 12 98 .226 .49 50 4400 9230 56 61 317 322 0 168 104 64 .186 170 66 5.39 .174 -2.43 -2.527 -2.43

Total number of rows: 43008

Table truncated, full table size 9325 Kbytes.




Supplementary data files not provided
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