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Sample GSM91921 Query DataSets for GSM91921
Status Public on Jan 12, 2006
Title LNCaPvsCRG
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 LNCaP total RNA
Organism Homo sapiens
Characteristics LNCaP total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35456.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) 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 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 1692 403 603 164 1089 239 1677 401 640 177 1074 237 0 0 323 144 195 117 100 78 98 50 1328 1311 4.556 .219 .221 .209 .235 1.912 52 245 .206 .58 80 1500 9420 50 58 38 46 0 278 113 165 .151 277 163 6.607 .152 -2.724 -2.716 -2.716
2 6510 12646 597 169 5913 12477 6614 12763 610 175 6017 12594 0 0 1952 3572 181 69 100 100 100 100 18390 18611 .474 2.11 2.093 2.181 2.039 1.445 52 296 2.095 .96 90 1640 9420 49 58 51 60 0 8721 117 8605 1.455 8802 8686 .687 1.443 .541 .53 .53
3 4261 2880 596 164 3665 2716 4080 2559 598 173 3484 2395 0 0 2093 1328 134 69 100 100 100 100 6381 5879 1.349 .741 .687 .83 .779 1.69 32 210 .669 .9 70 1790 9420 50 57 67 74 0 1986 113 1873 .511 1765 1652 1.957 .474 -.968 -1.077 -1.077
4 1973 1622 577 172 1396 1450 1955 1567 592 175 1378 1395 0 0 507 450 156 75 100 100 100 100 2846 2773 .963 1.039 1.012 1.062 .988 1.407 32 224 1.05 .87 70 1940 9410 49 56 82 89 0 1119 119 1000 .716 1081 962 1.396 .698 -.481 -.518 -.518
5 3365 2677 567 164 2798 2513 3383 2573 590 174 2816 2409 0 0 1012 713 171 69 100 100 100 100 5311 5225 1.113 .898 .855 .937 .871 1.426 52 333 .84 .93 90 2080 9420 49 58 95 104 0 1846 113 1733 .619 1774 1661 1.614 .59 -.691 -.761 -.761
6 2264 554 560 169 1704 385 2248 527 568 175 1688 358 0 0 422 156 125 68 100 96 100 96 2089 2046 4.426 .226 .212 .227 .238 1.453 32 220 .201 .82 70 2230 9410 49 56 111 118 0 382 117 266 .156 363 247 6.418 .146 -2.682 -2.773 -2.773
7 4637 3994 556 165 4081 3829 4763 3916 569 170 4207 3751 0 0 887 1200 124 74 100 100 100 100 7910 7958 1.066 .938 .892 .91 1.001 1.387 52 325 .987 .93 90 2380 9410 48 57 125 134 0 2754 114 2641 .647 2701 2587 1.545 .615 -.628 -.702 -.702
8 2025 1626 552 159 1473 1467 2038 1591 567 162 1486 1432 0 0 537 555 151 64 98 100 96 100 2940 2918 1.004 .996 .964 .949 .965 1.522 52 289 .953 .88 90 2520 9410 48 57 139 148 0 1121 110 1012 .687 1097 988 1.456 .665 -.542 -.589 -.589
9 1959 738 534 156 1425 582 1935 732 544 164 1401 576 0 0 358 219 115 69 100 100 100 100 2007 1977 2.448 .408 .411 .393 .393 1.528 52 334 .368 .83 90 2660 9410 48 57 153 162 0 509 108 401 .282 505 397 3.55 .284 -1.828 -1.818 -1.818
10 1477 340 520 160 957 180 1512 305 533 170 992 145 0 0 287 107 131 75 100 81 100 46 1137 1137 5.317 .188 .146 .155 .203 2.317 32 204 .188 .68 70 2820 9400 48 55 170 177 0 234 110 124 .13 210 100 7.709 .101 -2.947 -3.31 -3.31
11 4667 1144 522 169 4145 975 4881 1146 557 174 4359 977 0 0 1139 263 244 84 100 100 100 100 5120 5336 4.251 .235 .224 .238 .243 1.328 52 308 .201 .89 90 2950 9410 48 57 182 191 0 789 117 672 .162 790 674 6.164 .155 -2.624 -2.694 -2.694
12 4882 13539 549 185 4333 13354 4774 15600 801 757 4225 15415 0 0 2990 6831 1005 2425 78 90 71 81 17687 19640 .324 3.082 3.649 3.526 3.13 1.549 32 221 2.801 .95 70 3090 9400 48 55 197 204 0 9337 128 9210 2.125 10759 10631 .47 2.516 1.088 1.331 1.331
13 2788 3112 524 183 2264 2929 2783 3250 705 585 2259 3067 0 0 712 894 853 2037 98 86 78 9 5193 5326 .773 1.294 1.358 1.305 1.246 1.402 52 278 1.307 .91 80 3260 9400 48 56 214 222 0 2146 126 2020 .892 2241 2115 1.121 .936 -.165 -.095 -.095
14 1483 545 539 167 944 378 1484 537 554 177 945 370 0 0 262 129 148 80 100 98 98 94 1322 1315 2.497 .4 .392 .384 .419 1.714 52 295 .336 .77 90 3400 9410 48 57 227 236 0 376 115 261 .276 370 255 3.621 .27 -1.856 -1.889 -1.889
15 3029 650 537 173 2492 477 3070 636 550 209 2533 463 0 0 867 246 120 361 98 67 97 16 2969 2996 5.224 .191 .183 .172 .181 1.855 80 375 .184 .87 110 3550 9410 47 58 241 252 0 448 119 329 .132 439 319 7.575 .126 -2.921 -2.988 -2.988
16 10506 26574 534 187 9972 26387 10634 28876 842 901 10100 28689 0 0 4570 10844 1425 3096 92 98 92 92 36359 38789 .378 2.646 2.84 2.852 2.801 1.692 52 244 2.644 .94 80 3670 9400 48 56 255 263 0 18327 129 18198 1.825 19914 19786 .548 1.959 .868 .97 .97
17 4769 2704 542 180 4227 2524 4862 2750 802 696 4320 2570 0 0 1951 751 1337 2765 88 44 80 0 6751 6890 1.675 .597 .595 .666 .567 1.758 52 273 .516 .93 80 3830 9410 49 57 271 279 0 1865 124 1741 .412 1897 1772 2.428 .41 -1.28 -1.285 -1.285
18 746 206 550 181 196 25 594 186 603 221 44 5 0 0 465 92 342 193 17 3 15 0 221 49 7.84 .128 .114 .304 .224 3.899 52 256 .371 .66 80 3990 9390 47 55 287 295 -50 142 125 17 .088 128 3 11.368 .078 -3.507 -3.674
19 4991 10586 537 188 4454 10398 4952 11397 588 217 4415 11209 0 0 1792 3165 449 188 100 100 98 100 14852 15624 .428 2.335 2.539 2.418 2.449 1.377 80 381 2.306 .93 110 4130 9410 47 58 299 310 0 7301 130 7171 1.61 7860 7730 .621 1.751 .687 .808 .808
20 3037 3336 527 187 2510 3149 2883 3196 555 231 2356 3009 0 0 1166 1336 247 260 96 98 95 96 5659 5365 .797 1.255 1.277 1.33 1.265 1.564 80 396 1.207 .91 110 4280 9410 47 58 314 325 0 2301 129 2172 .865 2204 2075 1.156 .881 -.209 -.183 -.183

Total number of rows: 43104

Table truncated, full table size 9880 Kbytes.




Supplementary data files not provided
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