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Sample GSM90045 Query DataSets for GSM90045
Status Public on Dec 30, 2005
Title PT195_3
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PT195_3
Organism Homo sapiens
Characteristics PT195_3
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29176.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
1 230 151 85 80 145 71 252 136 93 83 167 56 0 0 130 61 36 26 65 68 65 53 216 223 2.042 .49 .335 .484 .495 2.984 32 156 .427 .67 60 1880 8620 55 61 69 75 0 114 60 53 .368 102 42 2.716 .252 -1.442 -1.988
2 293 160 83 76 210 84 211 144 90 84 128 68 0 0 480 146 50 62 77 57 60 10 294 196 2.5 .4 .531 .537 .56 2.631 80 423 .647 .79 110 2010 8630 53 64 79 90 -100 120 57 63 .301 108 51 3.325 .399 -1.733 -1.324
3 1045 1115 79 81 966 1034 1101 1218 87 90 1022 1137 0 0 497 598 51 62 97 98 91 91 2000 2159 .934 1.07 1.113 1.057 1.199 2.456 80 422 1.124 .82 110 2170 8620 52 63 95 106 0 838 61 777 .805 916 855 1.243 .836 -.313 -.258
4 2264 5381 82 82 2182 5299 2111 3193 84 86 2029 3111 0 0 1893 4922 24 30 92 100 92 100 7481 5140 .412 2.429 1.533 2.265 2.435 4.067 52 250 2.842 .86 80 2310 8620 54 62 111 119 0 4046 62 3984 1.826 2401 2339 .548 1.153 .869 .205
5 275 336 82 82 193 254 261 265 86 88 179 183 0 0 193 221 28 40 75 81 68 68 447 362 .76 1.316 1.022 1.334 1.199 3.272 32 137 1.352 .81 60 2470 8620 55 61 128 134 0 253 62 191 .99 199 138 1.011 .769 -.015 -.38
6 138 101 80 81 58 20 116 92 82 84 36 11 0 0 72 37 22 28 57 38 46 13 78 47 2.9 .345 .306 .611 .58 4.342 80 427 .386 .52 100 2580 8610 52 62 137 147 -50 76 61 15 .259 69 8 3.857 .23 -1.947 -2.122
7 574 390 82 78 492 312 598 397 84 81 516 319 0 0 330 240 22 26 84 84 84 75 804 835 1.577 .634 .618 .584 .67 3.218 52 273 .647 .84 80 2750 8610 53 61 155 163 0 293 59 235 .477 298 240 2.097 .465 -1.069 -1.105
8 2355 4520 83 80 2272 4440 1163 2351 173 113 1080 2271 0 0 2338 4514 710 310 63 91 46 77 6712 3351 .512 1.954 2.103 1.986 2.188 3.637 80 379 2.075 .75 100 2890 8620 53 63 168 178 0 3398 60 3338 1.469 1768 1708 .681 1.581 .555 .661
9 571 721 83 86 488 635 505 534 84 86 422 448 0 0 432 558 20 23 80 90 78 84 1123 870 .769 1.301 1.062 1.373 1.248 3.701 52 211 1.347 .81 80 3030 8630 55 63 183 191 0 542 65 477 .978 402 337 1.022 .798 -.032 -.325
10 129 106 82 81 47 25 109 92 84 84 27 11 0 0 71 48 22 23 51 42 36 28 72 38 1.88 .532 .407 .732 .786 3.325 80 354 .496 .46 100 3170 8610 52 62 196 206 -50 80 61 19 .4 69 8 2.5 .306 -1.322 -1.707
11 1132 1267 81 80 1051 1187 1221 1409 87 88 1140 1329 0 0 523 653 42 67 98 100 97 93 2238 2469 .885 1.129 1.166 1.081 1.135 2.213 80 451 1.182 .86 110 3320 8610 51 62 210 221 0 953 60 892 .849 1059 999 1.178 .877 -.236 -.19
12 490 651 80 80 410 571 368 698 91 92 288 618 0 0 364 458 53 87 78 76 71 67 981 906 .718 1.393 2.146 1.332 1.232 3.963 52 249 1.359 .85 80 3470 8630 55 63 227 235 0 489 60 429 1.047 525 465 .955 1.613 .066 .69
13 376 579 81 79 295 500 377 616 85 81 296 537 0 0 214 348 22 21 84 96 84 92 795 833 .59 1.695 1.814 1.435 1.462 2.949 52 241 1.884 .76 80 3610 8630 55 63 241 249 0 435 59 376 1.274 463 404 .785 1.364 .35 .448
14 182 159 81 80 101 79 189 165 84 84 108 85 0 0 93 62 23 24 71 75 68 68 180 193 1.278 .782 .787 .745 .789 3.277 32 170 .612 .6 60 3760 8620 55 61 257 263 0 120 60 59 .588 124 64 1.7 .592 -.766 -.757
15 1809 2298 83 79 1726 2219 1694 1870 86 81 1611 1791 0 0 1310 1796 24 23 97 100 90 98 3945 3402 .778 1.286 1.112 1.332 1.351 3.863 80 350 1.412 .86 100 3910 8620 53 63 270 280 0 1728 59 1668 .967 1406 1347 1.035 .836 -.049 -.259
16 785 1602 82 83 703 1519 849 1704 85 86 767 1621 0 0 489 957 24 32 88 97 86 97 2222 2388 .463 2.161 2.113 2.357 2.171 3.528 80 400 2.382 .81 100 4050 8620 53 63 284 294 0 1205 62 1142 1.625 1281 1219 .616 1.589 .7 .668
17 202 213 84 84 118 129 214 219 89 99 130 135 0 0 44 58 28 48 100 91 83 75 247 265 .915 1.093 1.038 1.026 .925 2.039 12 104 1.771 .6 50 4220 8610 54 59 303 308 0 160 63 97 .822 165 102 1.217 .781 -.283 -.357
18 154 105 85 79 69 26 157 104 89 86 72 25 0 0 51 31 24 39 81 31 68 6 95 97 2.654 .377 .347 .431 .492 5.116 32 150 .224 .24 60 4360 8610 54 60 317 323 0 79 59 20 .283 78 19 3.53 .261 -1.82 -1.937
19 616 1319 83 83 533 1236 674 1500 84 87 591 1417 0 0 239 650 21 29 98 100 96 100 1769 2008 .431 2.319 2.398 2.185 2.382 2.081 80 411 2.74 .87 110 4490 8610 51 62 327 338 0 992 62 929 1.744 1128 1065 .574 1.803 .802 .85
20 131 110 84 84 47 26 120 101 86 86 36 17 0 0 56 39 20 24 61 42 47 17 73 53 1.808 .553 .472 .515 .614 3.315 80 318 .373 .31 100 4630 8610 52 62 342 352 -50 83 63 20 .416 76 13 2.404 .355 -1.266 -1.494

Total number of rows: 43008

Table truncated, full table size 8984 Kbytes.




Supplementary data files not provided
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