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Sample GSM90020 Query DataSets for GSM90020
Status Public on Dec 30, 2005
Title PT112_5
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PT112_5
Organism Homo sapiens
Characteristics PT112_5
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32281.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
1 321 88 88 64 233 24 344 94 96 66 256 30 0 0 145 30 35 23 81 56 78 25 257 286 9.708 .103 .117 .138 .139 2.556 32 208 .062 .31 70 1760 8160 68 75 64 71 0 152 110 41 .178 162 52 5.631 .202 -2.493 -2.307
2 267 105 87 63 180 42 304 102 96 67 217 39 0 0 127 47 54 26 75 63 71 36 222 256 4.286 .233 .18 .301 .244 3.367 52 239 .188 .53 80 1890 8180 70 78 77 85 0 181 109 72 .402 176 67 2.486 .31 -1.314 -1.69
3 2211 622 86 63 2125 559 2457 636 100 67 2371 573 0 0 1167 301 86 28 96 97 87 96 2684 2944 3.801 .263 .242 .292 .261 1.793 80 474 .243 .95 110 2030 8160 66 77 89 100 0 1072 109 964 .454 1097 988 2.205 .417 -1.141 -1.263
4 4103 3272 89 68 4014 3204 3413 2633 99 72 3324 2565 0 0 3590 2857 91 31 90 100 80 98 7218 5889 1.253 .798 .772 1.051 .917 2.341 52 326 .771 .93 90 2180 8160 67 76 105 114 0 5641 117 5524 1.376 4540 4422 .727 1.33 .461 .412
5 519 337 90 63 429 274 393 202 93 68 303 139 0 0 398 300 24 27 80 82 71 73 703 442 1.566 .639 .459 .678 .776 2.722 52 298 .672 .85 90 2340 8170 68 77 121 130 0 581 109 472 1.101 348 240 .908 .791 .139 -.338
6 299 111 92 65 207 46 291 107 94 69 199 42 0 0 141 53 32 28 90 57 82 38 253 241 4.5 .222 .211 .203 .21 2.512 52 264 .24 .63 80 2480 8170 69 77 136 144 0 191 112 79 .383 184 72 2.61 .364 -1.384 -1.458
7 843 314 92 69 751 245 749 317 97 75 657 248 0 0 625 165 45 43 82 92 80 75 996 905 3.065 .326 .377 .383 .296 2.805 52 289 .258 .87 90 2620 8160 67 76 149 158 0 541 119 422 .562 547 428 1.778 .651 -.83 -.62
8 5716 3326 91 67 5625 3259 4716 3019 97 74 4625 2952 0 0 4588 2515 43 40 98 100 96 98 8884 7577 1.726 .579 .638 .603 .583 2.273 52 339 .553 .97 90 2760 8160 67 76 163 172 0 5734 116 5619 .999 5205 5090 1.001 1.1 -.002 .138
9 925 820 92 66 833 754 919 763 95 70 827 697 0 0 694 629 24 26 88 98 84 82 1587 1524 1.105 .905 .843 .95 .808 2.297 52 286 .897 .9 90 2920 8160 67 76 179 188 0 1414 114 1300 1.561 1316 1202 .641 1.453 .642 .539
10 148 103 90 63 58 40 120 94 101 69 30 31 0 0 79 48 66 31 33 48 20 23 98 61 1.45 .69 1.033 .662 .557 2.349 80 342 .212 .49 100 3050 8160 67 77 192 202 -50 178 109 69 1.189 162 53 .841 1.782 .25 .833
11 1894 769 96 64 1798 705 2000 756 114 70 1904 692 0 0 948 385 114 29 95 98 88 97 2503 2596 2.55 .392 .363 .419 .417 1.978 80 445 .346 .91 110 3200 8150 65 76 206 217 0 1326 110 1216 .676 1303 1193 1.479 .627 -.565 -.674
12 1113 437 96 73 1017 364 1072 361 120 76 976 288 0 0 814 324 118 30 75 90 75 78 1381 1264 2.794 .358 .295 .341 .35 1.798 32 209 .333 .9 70 3340 8160 68 75 222 229 0 753 126 628 .617 622 497 1.62 .509 -.696 -.975
13 632 276 94 67 538 209 653 266 107 72 559 199 0 0 418 147 75 31 76 86 75 84 747 758 2.574 .388 .356 .466 .378 2.443 52 259 .329 .89 80 3490 8170 69 77 237 245 0 476 116 360 .67 459 343 1.493 .614 -.578 -.704
14 225 168 92 66 133 102 244 179 95 70 152 113 0 0 86 68 24 27 84 81 81 75 235 265 1.304 .767 .743 .726 .818 1.921 32 156 .768 .73 60 3660 8160 69 75 255 261 0 290 114 176 1.322 309 195 .756 1.282 .403 .358
15 3059 1134 88 69 2971 1065 2881 1106 90 72 2793 1037 0 0 2000 708 23 25 97 100 96 98 4036 3830 2.79 .358 .371 .407 .368 2.362 80 381 .327 .9 100 3790 8160 67 77 266 276 0 1955 119 1836 .618 1907 1788 1.618 .64 -.694 -.644
16 1461 1055 83 62 1378 993 1544 1039 87 66 1461 977 0 0 1025 669 23 25 91 97 90 96 2371 2438 1.388 .721 .669 .927 .713 2.387 80 384 .682 .95 100 3940 8160 67 77 281 291 0 1819 107 1712 1.242 1791 1684 .805 1.153 .313 .205
17 206 128 85 62 121 66 217 126 90 65 132 64 0 0 70 38 24 23 90 84 87 65 187 196 1.833 .545 .485 .472 .526 2.143 32 224 .467 .58 70 4090 8150 67 74 297 304 0 221 107 114 .94 217 110 1.063 .836 -.089 -.259
18 213 78 89 63 124 15 231 75 93 66 142 12 0 0 67 27 29 21 87 43 84 9 139 154 8.267 .121 .085 .179 .199 2.943 32 185 .104 .27 70 4240 8150 67 74 312 319 0 134 109 26 .209 129 21 4.795 .146 -2.261 -2.779
19 1133 849 83 65 1050 784 1196 847 90 69 1113 782 0 0 333 244 34 26 100 100 100 100 1834 1895 1.339 .747 .703 .755 .734 1.339 80 427 .736 .95 110 4360 8150 65 76 322 333 0 1464 112 1352 1.287 1460 1348 .777 1.211 .364 .277
20 235 104 87 69 148 35 239 102 92 71 152 33 0 0 67 26 27 26 98 59 92 23 183 185 4.229 .236 .217 .235 .218 2.827 52 256 .209 .47 80 4520 8160 68 76 340 348 0 179 119 60 .408 176 57 2.453 .374 -1.294 -1.418

Total number of rows: 43008

Table truncated, full table size 8942 Kbytes.




Supplementary data files not provided
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