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Sample GSM90014 Query DataSets for GSM90014
Status Public on Dec 30, 2005
Title PN316_1
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PN316_1
Organism Homo sapiens
Characteristics PN316_1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, Non-tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24154.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)
GSE3933 Prostate Cancer

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
1 318 153 110 68 208 85 319 134 127 73 209 66 0 0 154 82 66 23 75 75 68 65 293 275 2.447 .409 .316 .433 .465 1.808 32 149 .342 .68 60 1710 8430 92 98 80 86 0 133 59 74 .355 117 57 2.814 .275 -1.493 -1.865
2 237 90 116 70 121 20 253 90 126 73 137 20 0 0 93 23 55 20 73 48 61 17 141 157 6.05 .165 .146 .24 .204 3.836 52 245 .12 .36 80 1870 8420 90 98 95 103 0 78 61 17 .144 78 17 6.958 .127 -2.799 -2.978
3 794 966 116 72 678 894 887 1094 117 73 771 1022 0 0 379 446 26 19 92 99 90 98 1572 1793 .758 1.319 1.326 1.395 1.222 2.357 120 471 1.293 .91 120 2010 8430 89 101 107 119 0 840 63 777 1.147 951 889 .872 1.153 .197 .205
4 1836 5046 119 76 1717 4970 1454 3915 121 79 1335 3839 0 0 1539 4168 26 22 92 100 88 100 6687 5174 .345 2.895 2.876 3.825 3.05 3.839 52 257 3.082 .89 90 2170 8440 91 100 124 133 0 4388 66 4322 2.517 3404 3338 .397 2.501 1.332 1.322
5 324 433 122 74 202 359 253 401 123 75 131 327 0 0 220 300 27 20 75 90 71 80 561 458 .563 1.777 2.496 1.545 1.54 2.616 52 218 1.779 .79 80 2320 8440 92 100 140 148 0 377 64 312 1.545 349 284 .647 2.171 .628 1.118
6 224 91 119 71 105 20 222 93 120 74 103 22 0 0 83 33 27 19 75 50 67 25 125 125 5.25 .19 .214 .323 .309 3.387 52 257 .203 .47 80 2450 8440 92 100 153 161 0 79 62 17 .166 81 19 6.038 .186 -2.594 -2.429
7 397 266 123 82 274 184 423 278 124 84 300 196 0 0 186 106 27 22 82 86 78 84 458 496 1.489 .672 .653 .671 .542 1.995 52 269 .523 .77 80 2600 8420 90 98 168 176 0 231 71 160 .584 242 170 1.713 .568 -.776 -.816
8 1988 2089 119 82 1869 2007 1540 1553 123 83 1421 1471 0 0 1643 1382 31 23 98 100 92 100 3876 2892 .931 1.074 1.035 1.468 1.039 2.893 80 401 .955 .92 100 2750 8430 90 100 182 192 0 1817 71 1745 .934 1350 1279 1.071 .9 -.099 -.152
9 561 930 121 84 440 846 671 1046 126 102 550 962 0 0 351 547 35 94 76 82 76 75 1286 1512 .52 1.923 1.749 1.894 1.705 2.811 52 328 1.89 .85 90 2900 8430 90 99 197 206 0 809 73 736 1.672 910 837 .598 1.521 .742 .605
10 236 725 112 94 124 631 255 734 130 156 143 640 0 0 81 197 52 173 83 100 58 83 755 783 .197 5.089 4.476 4.287 3.793 1.619 12 84 4.886 .78 50 3060 8430 92 97 215 220 0 630 82 549 4.425 638 557 .226 3.892 2.146 1.96
11 810 540 115 75 695 465 854 556 120 87 739 481 0 0 351 224 33 77 95 93 93 87 1160 1220 1.495 .669 .651 .675 .649 2.123 120 589 .636 .9 120 3180 8420 88 100 224 236 0 470 65 404 .582 483 418 1.719 .566 -.781 -.821
12 700 476 111 73 589 403 749 579 116 79 638 506 0 0 377 232 31 45 84 87 81 84 992 1144 1.462 .684 .793 .864 .695 4.075 32 212 .624 .79 70 3340 8420 90 97 242 249 0 414 63 350 .595 503 440 1.681 .69 -.749 -.536
13 419 370 114 77 305 293 386 425 117 81 272 348 0 0 244 205 26 21 80 82 76 78 598 620 1.041 .961 1.279 1.038 .889 3.285 52 265 .874 .79 80 3480 8420 90 98 256 264 0 322 67 255 .835 370 303 1.197 1.113 -.26 .154
14 241 124 116 80 125 44 257 123 118 82 141 43 0 0 82 31 26 22 84 78 84 37 169 184 2.841 .352 .305 .281 .283 2.824 32 150 .265 .55 60 3640 8420 91 97 273 279 0 108 70 38 .306 107 37 3.267 .265 -1.708 -1.915
15 1414 1897 120 86 1294 1811 1514 1735 121 86 1394 1649 0 0 790 1248 27 23 96 100 95 100 3105 3043 .715 1.4 1.183 1.231 1.402 2.327 80 345 1.595 .89 100 3770 8430 90 100 284 294 0 1650 75 1575 1.217 1509 1434 .822 1.029 .283 .041
16 761 1220 116 88 645 1132 720 1227 122 90 604 1139 0 0 415 621 37 27 91 98 91 97 1777 1743 .57 1.755 1.886 1.851 1.65 2.523 80 421 1.753 .88 110 3910 8430 89 100 297 308 0 1061 77 984 1.526 1067 990 .655 1.64 .61 .714
17 240 236 119 85 121 151 245 239 124 92 126 154 0 0 75 73 31 38 87 90 87 87 272 280 .801 1.248 1.222 1.044 1.172 2.192 32 165 1.415 .64 60 4070 8410 90 96 316 322 0 205 74 131 1.085 208 134 .922 1.063 .118 .088
18 192 97 121 81 71 16 199 95 121 86 78 14 0 0 59 29 26 34 75 26 63 1 87 92 4.438 .225 .179 .234 .243 5.16 52 246 .135 .13 80 4210 8420 90 98 329 337 0 84 70 14 .196 83 12 5.103 .156 -2.351 -2.68
19 476 570 123 81 353 489 511 618 124 84 388 537 0 0 182 244 29 28 91 98 88 91 842 925 .722 1.385 1.384 1.258 1.284 2.272 80 465 1.41 .84 110 4350 8410 87 98 341 352 0 496 70 425 1.205 537 467 .83 1.203 .269 .267
20 268 130 128 87 140 43 279 118 135 87 151 31 0 0 64 48 41 22 91 50 83 50 183 182 3.256 .307 .205 .272 .371 2.895 12 98 .209 .33 50 4510 8420 91 96 360 365 0 113 76 37 .267 103 27 3.744 .179 -1.905 -2.486

Total number of rows: 43008

Table truncated, full table size 9119 Kbytes.




Supplementary data files not provided
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