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Sample GSM91916 Query DataSets for GSM91916
Status Public on Jan 12, 2006
Title PPCvsCRG
Sample type RNA
 
Channel 1
Source name CRG mRNA
Organism Homo sapiens
Characteristics CRG mRNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PPC total RNA
Organism Homo sapiens
Characteristics PPC total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35684.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 Jan 11, 2006
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 GPL3341
Series (2)
GSE4016 Gene expression variations in prostate cancer cell lines
GSE4396 Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 1315 498 227 116 1088 382 1271 428 242 129 1044 312 0 0 415 221 104 65 96 100 96 96 1470 1356 2.848 .351 .299 .305 .282 1.535 32 189 .315 .8 70 1860 9210 29 36 46 53 0 493 115 378 .348 424 309 2.877 .296 -1.524 -1.757 -1.757
2 9096 12695 227 131 8869 12564 9669 13071 232 135 9442 12940 0 0 2758 3494 59 62 100 100 100 100 21433 22382 .706 1.417 1.37 1.464 1.409 1.427 52 256 1.413 .95 80 2000 9200 28 36 60 68 0 12569 130 12440 1.403 12942 12812 .713 1.357 .488 .44 .44
3 3898 2479 226 126 3672 2353 3526 2418 234 136 3300 2292 0 0 4380 1544 73 61 100 98 96 94 6025 5592 1.561 .641 .695 .708 .737 2.262 52 276 .354 .67 80 2150 9200 28 36 75 83 0 2454 125 2330 .634 2394 2269 1.576 .688 -.656 -.54 -.54
4 1646 777 232 131 1414 646 1675 714 241 139 1443 583 0 0 379 311 65 61 100 100 100 100 2060 2026 2.189 .457 .404 .427 .436 1.72 32 207 .433 .8 70 2300 9190 27 34 90 97 0 769 130 640 .452 707 577 2.211 .4 -1.145 -1.322 -1.322
5 3189 2939 254 136 2935 2803 3256 2993 258 140 3002 2857 0 0 1116 915 81 59 100 100 100 100 5738 5859 1.047 .955 .952 .982 .903 1.457 52 267 .903 .91 80 2440 9200 28 36 104 112 0 2910 135 2775 .946 2963 2829 1.058 .942 -.081 -.086 -.086
6 1856 1433 251 142 1605 1291 1874 1413 253 144 1623 1271 0 0 662 497 85 58 100 100 100 100 2896 2894 1.243 .804 .783 .826 .789 1.669 52 254 .781 .92 80 2590 9200 28 36 119 127 0 1419 141 1278 .796 1399 1258 1.256 .775 -.328 -.367 -.367
7 2741 974 242 142 2499 832 3007 1019 241 145 2765 877 0 0 1180 375 73 61 98 100 98 98 3331 3642 3.004 .333 .317 .358 .333 1.985 52 254 .293 .87 80 2740 9200 28 36 134 142 0 964 141 824 .33 1009 868 3.034 .314 -1.601 -1.671 -1.671
8 1655 2090 241 137 1414 1953 1660 2195 248 145 1419 2058 0 0 508 731 70 64 100 100 100 100 3367 3477 .724 1.381 1.45 1.338 1.399 1.552 52 245 1.418 .9 80 2880 9200 28 36 148 156 0 2069 136 1934 1.368 2173 2038 .731 1.436 .452 .522 .522
9 1324 767 237 142 1087 625 1325 771 246 154 1088 629 0 0 278 215 66 61 100 100 100 100 1712 1717 1.739 .575 .578 .555 .626 1.466 52 320 .539 .89 90 3020 9200 27 36 161 170 0 759 141 619 .569 763 623 1.757 .572 -.813 -.805 -.805
10 1037 331 251 139 786 192 1007 339 252 145 756 200 0 0 256 139 66 60 100 84 100 65 978 956 4.094 .244 .265 .227 .253 2.248 32 196 .244 .67 70 3180 9210 29 36 178 185 0 328 138 190 .242 336 198 4.135 .262 -2.048 -1.933 -1.933
11 5193 914 260 141 4933 773 4892 839 306 150 4632 698 0 0 1569 288 638 79 100 100 100 100 5706 5330 6.382 .157 .151 .155 .153 1.496 52 272 .135 .89 80 3310 9210 29 37 191 199 0 905 140 765 .155 831 691 6.445 .149 -2.688 -2.745 -2.745
12 10807 8649 257 147 10550 8502 10470 8748 275 169 10213 8601 0 0 4359 2811 129 96 100 100 100 100 19052 18814 1.241 .806 .842 .823 .814 1.466 32 215 .76 .92 70 3460 9200 28 35 206 213 0 8563 146 8418 .798 8661 8516 1.253 .834 -.326 -.262 -.262
13 2109 486 254 151 1855 335 2177 443 275 232 1923 292 0 0 769 157 141 835 98 0 96 0 2190 2215 5.537 .181 .152 .19 .179 1.829 80 386 .153 .79 100 3610 9210 28 38 220 230 0 481 150 332 .179 439 289 5.593 .15 -2.484 -2.734 -2.734
14 1083 330 252 149 831 181 1099 329 263 158 847 180 0 0 221 115 69 68 100 80 100 57 1012 1027 4.591 .218 .213 .189 .235 2.494 52 290 .186 .58 90 3760 9210 28 37 235 244 0 327 148 179 .216 326 178 4.637 .21 -2.213 -2.249 -2.249
15 2135 624 240 150 1895 474 2215 584 260 156 1975 434 0 0 490 258 100 66 98 98 98 94 2369 2409 3.998 .25 .22 .242 .221 2.214 52 274 .228 .8 90 3900 9210 28 37 249 258 0 618 149 469 .248 578 430 4.038 .218 -2.014 -2.2 -2.2
16 13728 23086 248 155 13480 22931 14475 22673 281 183 14227 22518 0 0 3634 6355 235 247 100 100 100 100 36411 36745 .588 1.701 1.583 1.711 1.68 1.263 52 320 1.698 .96 90 4040 9210 28 37 263 272 0 22857 153 22704 1.684 22449 22295 .594 1.567 .752 .648 .648
17 4899 3395 244 159 4655 3236 4662 3324 281 189 4418 3165 0 0 1212 857 251 270 100 100 100 100 7891 7583 1.439 .695 .716 .692 .732 1.359 52 261 .685 .94 80 4200 9210 29 37 280 288 0 3361 157 3204 .688 3291 3134 1.453 .709 -.539 -.496 -.496
18 360 198 236 155 124 43 258 149 243 165 22 -6 0 0 318 130 78 75 26 25 15 13 167 16 2.884 .347 null .886 .854 3.633 52 236 .285 .47 80 4350 9200 28 36 295 303 -50 196 153 43 .343 148 null 2.913 null -1.542 null
19 3510 6148 246 156 3264 5992 3713 6367 250 164 3467 6211 0 0 1472 2151 75 75 97 100 96 100 9256 9678 .545 1.836 1.791 2.039 1.851 1.751 80 324 1.793 .95 100 4490 9220 29 39 308 318 0 6087 154 5933 1.818 6304 6150 .55 1.774 .862 .827 .827
20 2555 2774 241 152 2314 2622 2628 2751 263 167 2387 2599 0 0 715 660 115 92 100 100 98 100 4936 4986 .883 1.133 1.089 1.185 1.139 1.514 52 290 1.09 .94 90 4630 9210 28 37 322 331 0 2747 150 2596 1.122 2724 2573 .891 1.078 .166 .108 .108

Total number of rows: 43104

Table truncated, full table size 9752 Kbytes.




Supplementary data files not provided
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