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Sample GSM91917 Query DataSets for GSM91917
Status Public on Jan 12, 2006
Title PC3vsCRG
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 PC3 total RNA
Organism Homo sapiens
Characteristics PC3 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35461.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 1244 828 382 165 862 663 1255 767 390 172 873 602 0 0 440 327 88 70 98 98 90 98 1525 1475 1.3 .769 .69 .831 .717 1.955 52 246 .718 .83 80 1910 9330 41 49 43 51 0 690 138 553 .641 639 502 1.56 .575 -.642 -.799 -.799
2 4813 1138 376 171 4437 967 5048 1136 391 178 4672 965 0 0 1603 337 93 79 100 100 100 98 5404 5637 4.588 .218 .207 .22 .215 1.337 52 253 .207 .94 80 2050 9320 40 48 57 65 0 948 143 806 .182 947 804 5.506 .172 -2.461 -2.538 -2.538
3 4040 3504 406 183 3634 3321 3897 3506 409 191 3491 3323 0 0 1871 1566 94 86 100 100 96 100 6955 6814 1.094 .914 .952 .979 .925 1.559 32 211 .878 .96 70 2200 9320 40 47 72 79 0 2920 153 2768 .762 2922 2769 1.313 .793 -.393 -.334 -.334
4 1675 1181 416 170 1259 1011 1751 1171 430 183 1335 1001 0 0 568 381 128 70 100 100 96 100 2270 2336 1.245 .803 .75 .829 .838 1.583 32 212 .746 .86 70 2350 9310 39 46 87 94 0 984 142 843 .669 976 834 1.494 .625 -.58 -.678 -.678
5 2687 2148 409 183 2278 1965 2721 2159 408 188 2312 1976 0 0 930 593 94 70 100 100 98 100 4243 4288 1.159 .863 .855 .935 .852 1.616 52 332 .782 .93 90 2490 9310 38 47 100 109 0 1790 153 1638 .719 1799 1647 1.391 .712 -.476 -.49 -.49
6 1565 1223 415 176 1150 1047 1534 1254 425 187 1119 1078 0 0 288 282 99 75 100 100 100 100 2197 2197 1.098 .91 .963 .9 .936 1.413 32 209 .899 .89 70 2640 9310 39 46 116 123 0 1019 147 873 .759 1045 898 1.318 .803 -.398 -.317 -.317
7 3322 3485 404 175 2918 3310 3574 3640 415 181 3170 3465 0 0 1022 963 93 68 100 100 100 100 6228 6635 .882 1.134 1.093 1.185 1.153 1.432 52 271 1.05 .93 80 2780 9320 40 48 130 138 0 2904 146 2758 .945 3033 2888 1.058 .911 -.081 -.135 -.135
8 1491 1855 406 173 1085 1682 1466 1895 417 183 1060 1722 0 0 402 565 116 76 100 100 100 100 2767 2782 .645 1.55 1.625 1.562 1.534 1.487 52 251 1.592 .91 80 2940 9320 40 48 146 154 0 1546 144 1402 1.292 1579 1435 .774 1.354 .369 .437 .437
9 1371 1066 395 171 976 895 1366 1068 402 182 971 897 0 0 376 362 100 74 98 100 97 98 1871 1868 1.091 .917 .924 .908 .942 1.558 80 350 .896 .9 100 3080 9320 39 49 159 169 0 888 143 746 .764 890 748 1.309 .77 -.388 -.377 -.377
10 992 502 378 169 614 333 999 498 382 177 621 329 0 0 229 133 88 67 100 96 96 96 947 950 1.844 .542 .53 .538 .505 1.745 32 192 .468 .8 70 3230 9310 39 46 175 182 0 418 141 278 .452 415 274 2.213 .441 -1.146 -1.18 -1.18
11 3633 1422 375 168 3258 1254 3668 1436 424 257 3293 1268 0 0 1401 544 357 599 98 88 96 55 4512 4561 2.598 .385 .385 .379 .375 1.465 80 392 .357 .9 100 3370 9320 39 49 188 198 0 1185 140 1045 .321 1197 1057 3.118 .321 -1.64 -1.64 -1.64
12 6802 8876 372 169 6430 8707 6431 6740 442 310 6059 6571 0 0 5404 7571 423 746 86 88 84 76 15137 12630 .738 1.354 1.085 1.385 1.293 1.877 52 249 1.417 .95 80 3540 9310 39 47 206 214 0 7397 141 7256 1.128 5617 5476 .886 .904 .174 -.146 -.146
13 2062 724 381 178 1681 546 1950 741 390 184 1569 563 0 0 680 202 87 75 100 100 100 100 2227 2132 3.079 .325 .359 .329 .319 1.612 80 312 .288 .87 100 3670 9320 39 49 218 228 0 603 148 455 .271 618 469 3.695 .299 -1.885 -1.742 -1.742
14 1171 496 396 185 775 311 1196 503 407 189 800 318 0 0 248 207 95 75 100 88 96 77 1086 1118 2.492 .401 .398 .365 .418 1.854 80 332 .417 .77 100 3820 9320 39 49 233 243 0 413 154 259 .334 419 265 2.99 .331 -1.58 -1.594 -1.594
15 2473 663 392 182 2081 481 2495 662 403 188 2103 480 0 0 408 160 99 70 100 100 100 100 2562 2583 4.326 .231 .228 .222 .229 1.46 80 305 .218 .86 100 3970 9320 39 49 248 258 0 553 152 401 .193 552 400 5.192 .19 -2.376 -2.394 -2.394
16 11605 23030 392 180 11213 22850 12235 23124 402 189 11843 22944 0 0 5578 9427 104 71 100 100 100 100 34063 34787 .491 2.038 1.937 2.183 2.029 1.456 80 334 1.987 .96 100 4100 9320 39 49 261 271 0 19192 150 19042 1.698 19270 19120 .589 1.614 .764 .691 .691
17 3783 3799 373 180 3410 3619 3672 3751 380 186 3299 3571 0 0 1489 1002 101 70 98 100 98 100 7029 6870 .942 1.061 1.082 1.183 1.068 1.756 52 288 .978 .93 90 4250 9320 39 48 276 285 0 3166 150 3016 .884 3126 2976 1.131 .902 -.177 -.149 -.149
18 529 249 365 184 164 65 420 217 372 193 55 33 0 0 313 118 88 73 40 32 21 15 229 88 2.523 .396 .6 .582 .556 3.456 52 246 .258 .45 80 4400 9310 39 47 292 300 -50 208 153 54 .33 181 28 3.028 .5 -1.598 -1
19 3746 7551 363 182 3383 7369 3696 7778 368 191 3333 7596 0 0 1043 1596 89 77 100 100 100 100 10752 10929 .459 2.178 2.279 2.237 2.238 1.281 80 337 2.151 .95 100 4550 9320 39 49 306 316 0 6293 152 6141 1.815 6482 6330 .551 1.899 .86 .925 .925
20 2580 2379 372 187 2208 2192 2462 2327 423 197 2090 2140 0 0 935 804 337 83 98 100 97 100 4400 4230 1.007 .993 1.024 1.04 1.001 1.654 80 327 .959 .93 100 4700 9320 39 49 321 331 0 1983 156 1827 .827 1939 1783 1.209 .853 -.274 -.229 -.229

Total number of rows: 43104

Table truncated, full table size 9863 Kbytes.




Supplementary data files not provided
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