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Sample GSM91922 Query DataSets for GSM91922
Status Public on Jan 12, 2006
Title 22Rv1vsCRG
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 22Rv1 total RNA
Organism Homo sapiens
Characteristics 22Rv1 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35464.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 1211 343 396 160 815 183 1236 324 404 171 840 164 0 0 342 149 106 82 98 78 92 50 998 1004 4.454 .225 .195 .224 .25 2.56 52 232 .166 .49 80 1740 9070 55 63 38 46 0 250 117 134 .164 236 120 6.101 .143 -2.609 -2.811 -2.811
2 6107 9735 389 163 5718 9572 6390 10152 397 177 6001 9989 0 0 2067 3237 103 82 100 100 100 100 15290 15990 .597 1.674 1.665 1.694 1.716 1.555 52 307 1.696 .91 90 1880 9060 53 62 51 60 0 7106 119 6987 1.222 7410 7291 .818 1.215 .289 .281 .281
3 3827 1901 397 165 3430 1736 3361 1527 405 179 2964 1362 0 0 2247 1205 96 78 100 100 100 96 5166 4326 1.976 .506 .46 .505 .501 2.358 32 212 .428 .82 70 2040 9060 54 61 68 75 0 1388 120 1267 .369 1115 994 2.707 .335 -1.437 -1.576 -1.576
4 1379 967 389 167 990 800 1360 1034 390 179 971 867 0 0 487 360 87 78 98 98 94 98 1790 1838 1.238 .808 .893 .826 .773 2.229 52 245 .749 .85 80 2180 9060 54 62 82 90 0 706 122 584 .59 755 633 1.695 .652 -.762 -.618 -.618
5 2641 2258 400 166 2241 2092 2583 2189 404 182 2183 2023 0 0 951 739 113 92 100 100 100 100 4333 4206 1.071 .934 .927 .978 .885 1.726 52 298 .872 .83 90 2320 9060 53 62 95 104 0 1648 121 1527 .681 1598 1477 1.468 .676 -.553 -.564 -.564
6 2318 2424 419 178 1899 2246 2253 2545 423 199 1834 2367 0 0 556 754 109 121 100 100 100 100 4145 4201 .846 1.183 1.291 1.145 1.255 1.534 32 220 1.205 .89 70 2470 9050 53 60 111 118 0 1769 130 1639 .863 1858 1728 1.158 .942 -.212 -.086 -.086
7 3878 2160 402 179 3476 1981 4363 2265 411 193 3961 2086 0 0 1242 639 108 106 98 100 98 100 5457 6047 1.755 .57 .527 .576 .563 1.446 52 260 .539 .94 80 2630 9060 54 62 127 135 0 1577 131 1446 .416 1653 1523 2.404 .384 -1.265 -1.379 -1.379
8 1656 555 396 187 1260 368 1576 551 418 194 1180 364 0 0 615 178 117 83 100 98 98 88 1628 1544 3.424 .292 .308 .298 .273 1.931 52 232 .241 .77 80 2760 9060 54 62 140 148 0 405 136 269 .213 402 266 4.691 .225 -2.23 -2.151 -2.151
9 1825 1073 411 194 1414 879 1813 1089 1005 353 1402 895 0 0 397 311 3610 941 0 38 0 1 2293 2297 1.609 .622 .638 .61 .575 1.447 52 314 .439 .87 90 2910 9060 53 62 154 163 0 783 142 642 .454 795 653 2.204 .466 -1.14 -1.102 -1.102
10 1723 743 411 186 1312 557 1739 639 422 193 1328 453 0 0 564 352 114 91 100 93 96 90 1869 1781 2.355 .425 .341 .368 .389 2.2 32 201 .378 .74 70 3050 9050 53 60 169 176 0 542 136 407 .31 466 331 3.227 .249 -1.69 -2.006 -2.006
11 4411 1211 431 201 3980 1010 4524 1222 464 220 4093 1021 0 0 1484 494 268 133 100 98 100 92 4990 5114 3.941 .254 .249 .24 .249 1.605 52 330 .218 .86 90 3190 9050 52 61 182 191 0 884 147 737 .185 892 745 5.399 .182 -2.433 -2.457 -2.457
12 7796 28436 440 210 7356 28226 7347 26273 614 730 6907 26063 0 0 4226 15919 864 2669 93 93 90 90 35582 32970 .261 3.837 3.773 3.959 3.867 1.869 32 215 4.063 .92 70 3330 9040 52 59 197 204 0 20756 153 20603 2.801 19177 19024 .357 2.754 1.486 1.462 1.462
13 2558 1378 403 185 2155 1193 2318 1369 503 458 1915 1184 0 0 1045 627 695 1979 97 11 76 0 3348 3099 1.806 .554 .618 .504 .541 1.855 80 398 .493 .85 100 3500 9050 52 62 213 223 0 1006 135 871 .404 999 864 2.475 .451 -1.307 -1.148 -1.148
14 1430 594 394 172 1036 422 1423 537 408 186 1029 365 0 0 284 231 104 83 100 98 100 90 1458 1394 2.455 .407 .355 .367 .382 1.776 52 233 .369 .72 80 3640 9050 53 61 228 236 0 434 126 308 .297 392 266 3.363 .259 -1.75 -1.949 -1.949
15 3651 892 412 203 3239 689 3857 840 436 205 3445 637 0 0 1042 272 140 83 100 100 100 100 3928 4082 4.701 .213 .185 .209 .214 1.61 52 274 .184 .85 90 3780 9050 52 61 241 250 0 651 148 503 .155 613 465 6.44 .135 -2.687 -2.889 -2.889
16 16067 20597 430 192 15637 20405 17301 22910 437 198 16871 22718 0 0 7297 9660 125 80 100 100 100 100 36042 39589 .766 1.305 1.347 1.259 1.287 1.658 80 377 1.32 .95 100 3930 9050 52 62 256 266 0 15034 140 14894 .952 16723 16582 1.05 .983 -.07 -.025 -.025
17 5916 4112 408 186 5508 3926 6128 4231 417 196 5720 4045 0 0 1696 1291 112 90 100 100 100 100 9434 9765 1.403 .713 .707 .703 .724 1.428 52 243 .709 .92 80 4080 9050 53 61 272 280 0 3001 136 2866 .52 3088 2953 1.922 .516 -.943 -.954 -.954
18 628 369 403 189 225 180 472 225 417 201 69 36 0 0 482 366 112 95 34 42 21 25 405 105 1.25 .8 .522 .773 .75 3.678 52 242 .663 .63 80 4230 9040 52 60 287 295 -50 269 138 131 .584 164 26 1.713 .381 -.776 -1.393
19 5609 13377 394 199 5215 13178 5583 14993 414 211 5189 14794 0 0 1971 5050 120 94 100 100 100 100 18393 19983 .396 2.527 2.851 2.442 2.466 1.492 80 349 2.622 .95 100 4370 9040 51 61 300 310 0 9764 145 9619 1.844 10944 10799 .542 2.081 .883 1.057 1.057
20 3640 3651 408 199 3232 3452 3801 3691 440 224 3393 3492 0 0 1094 1042 237 128 100 100 100 100 6684 6885 .936 1.068 1.029 1.08 1.077 1.352 52 300 1.013 .92 90 4510 9040 51 60 314 323 0 2665 145 2520 .78 2694 2549 1.283 .751 -.359 -.413 -.413

Total number of rows: 43104

Table truncated, full table size 9981 Kbytes.




Supplementary data files not provided
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