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Sample GSM90030 Query DataSets for GSM90030
Status Public on Dec 30, 2005
Title PT233_4
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PT233_4
Organism Homo sapiens
Characteristics PT233_4
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32287.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) array@genome.stanford.edu
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
1 590 178 113 66 477 112 650 180 115 68 537 114 0 0 250 72 35 21 88 82 86 82 589 651 4.259 .235 .212 .216 .243 1.678 52 291 .233 .87 80 1600 8290 81 89 40 48 0 287 106 181 .379 290 184 2.641 .342 -1.401 -1.546
2 467 120 117 66 350 54 511 124 120 68 394 58 0 0 205 45 27 19 88 76 86 69 404 452 6.481 .154 .147 .189 .177 2.317 52 301 .141 .73 90 1750 8290 80 89 54 63 0 194 106 87 .249 200 94 4.019 .237 -2.007 -2.074
3 2945 1309 120 72 2825 1237 3317 1414 133 74 3197 1342 0 0 980 408 78 26 100 100 100 100 4062 4539 2.284 .438 .42 .446 .447 1.386 80 388 .417 .97 100 1900 8290 80 90 69 79 0 2111 116 1995 .706 2281 2165 1.416 .677 -.502 -.563
4 4187 13113 123 78 4064 13035 3823 11340 137 81 3700 11262 0 0 3145 9957 86 27 98 100 90 100 17099 14962 .312 3.207 3.044 3.76 3.282 1.939 52 283 3.258 .98 90 2040 8290 80 89 83 92 0 21150 126 21024 5.173 18290 18165 .193 4.909 2.371 2.296
5 604 1481 124 75 480 1406 696 1643 127 76 572 1568 0 0 337 873 32 21 82 98 80 98 1886 2140 .341 2.929 2.741 3.171 2.916 1.952 52 311 2.92 .93 90 2180 8280 79 88 97 106 0 2389 121 2268 4.724 2650 2529 .212 4.421 2.24 2.144
6 516 156 124 72 392 84 556 159 126 75 432 87 0 0 235 55 35 21 94 80 86 75 476 519 4.667 .214 .201 .224 .222 1.996 52 290 .185 .79 80 2340 8280 80 88 114 122 0 252 116 135 .346 256 140 2.893 .325 -1.533 -1.622
7 1112 366 123 74 989 292 1214 357 127 75 1091 283 0 0 574 177 36 19 96 90 94 88 1281 1374 3.387 .295 .259 .284 .299 1.44 52 264 .28 .96 80 2480 8280 80 88 128 136 0 590 119 471 .476 576 456 2.1 .418 -1.07 -1.257
8 6434 6063 122 71 6312 5992 6704 6740 126 74 6582 6669 0 0 3862 3214 33 19 100 100 100 100 12304 13251 1.053 .949 1.013 1.058 .94 1.589 52 288 .887 .96 90 2630 8280 79 88 142 151 0 9779 115 9665 1.531 10871 10756 .653 1.634 .615 .709
9 1443 1011 125 76 1318 935 1539 1039 128 78 1414 963 0 0 730 424 32 21 98 100 96 100 2253 2377 1.41 .709 .681 .815 .699 1.705 52 318 .655 .94 90 2770 8280 79 88 156 165 0 1631 123 1508 1.144 1676 1553 .874 1.098 .194 .135
10 525 186 138 82 387 104 524 191 158 82 386 109 0 0 166 38 96 25 100 100 91 83 491 495 3.721 .269 .282 .274 .294 1.537 12 104 .214 .83 50 2900 8280 81 86 171 176 0 300 132 168 .433 308 176 2.307 .455 -1.206 -1.135
11 2478 1160 127 73 2351 1087 2529 1227 162 82 2402 1154 0 0 772 309 192 67 100 100 100 98 3438 3556 2.163 .462 .48 .469 .454 1.368 80 427 .425 .93 100 3060 8280 79 89 185 195 0 1871 118 1753 .746 1979 1861 1.341 .775 -.423 -.368
12 1571 745 133 79 1438 666 1630 728 173 92 1497 649 0 0 1075 489 217 78 82 84 75 76 2104 2146 2.159 .463 .434 .437 .463 1.868 52 325 .434 .94 90 3210 8280 79 88 200 209 0 1202 127 1074 .747 1174 1047 1.339 .699 -.421 -.516
13 1096 764 129 72 967 692 1081 781 138 77 952 709 0 0 650 408 62 33 84 98 84 92 1659 1661 1.397 .716 .745 .843 .729 2.368 52 247 .659 .92 80 3360 8280 80 88 216 224 0 1232 116 1116 1.154 1260 1144 .866 1.201 .207 .264
14 532 200 125 76 407 124 573 206 135 76 448 130 0 0 228 72 47 20 96 87 93 81 531 578 3.282 .305 .29 .265 .328 2.284 32 216 .253 .79 70 3490 8280 80 87 229 236 0 323 123 200 .491 332 210 2.035 .468 -1.025 -1.095
15 5321 3410 125 77 5196 3333 6158 3635 132 80 6033 3558 0 0 2869 1726 44 21 100 100 100 100 8529 9591 1.559 .641 .59 .701 .649 1.664 52 328 .625 .96 90 3650 8290 80 89 244 253 0 5500 124 5376 1.035 5863 5739 .967 .951 .049 -.072
16 2005 3072 124 76 1881 2996 2043 2882 130 80 1919 2806 0 0 1372 1894 47 32 95 100 90 100 4877 4725 .628 1.593 1.462 2.05 1.581 2.2 80 374 1.522 .97 100 3790 8280 79 89 258 268 0 4955 123 4832 2.569 4648 4526 .389 2.358 1.361 1.238
17 415 164 122 80 293 84 440 177 125 82 318 97 0 0 178 60 28 22 86 76 86 73 377 415 3.488 .287 .305 .275 .296 2.127 52 254 .277 .82 80 3930 8280 80 88 273 281 0 265 129 135 .462 285 156 2.163 .492 -1.113 -1.023
18 501 107 129 77 372 30 550 95 135 81 421 18 0 0 189 33 38 22 93 43 87 31 402 439 12.4 .081 .043 .066 .07 2.341 32 200 .069 .44 70 4070 8280 80 87 287 294 0 173 124 48 .13 153 29 7.688 .069 -2.943 -3.858
19 1210 1125 131 78 1079 1047 1329 1227 160 98 1198 1149 0 0 468 419 157 121 96 100 90 96 2126 2347 1.031 .97 .959 1.014 .997 1.398 80 469 .953 .94 110 4220 8270 77 88 300 311 0 1815 126 1689 1.565 1979 1853 .639 1.547 .646 .629
20 515 124 135 79 380 45 534 128 198 123 399 49 0 0 179 35 233 177 78 0 40 0 425 448 8.444 .118 .123 .121 .14 2.043 32 206 .571 .67 70 4360 8280 80 87 316 323 0 200 127 73 .191 206 79 5.236 .198 -2.388 -2.336

Total number of rows: 43008

Table truncated, full table size 9173 Kbytes.




Supplementary data files not provided
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