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Sample GSM91919 Query DataSets for GSM91919
Status Public on Jan 12, 2006
Title MDA2BvsCRG
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 MDA2B total RNA
Organism Homo sapiens
Characteristics MDA2B total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35633.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
1 732 106 264 54 468 52 745 93 265 56 481 39 0 0 308 51 69 18 87 71 84 50 520 520 9 .111 .081 .123 .115 3.186 32 170 .104 .73 60 2110 9410 22 28 28 34 0 120 61 59 .126 106 44 7.92 .092 -2.986 -3.44 -3.44
2 973 5398 253 60 720 5338 847 5680 260 91 594 5620 0 0 548 3736 76 243 87 90 78 87 6058 6214 .135 7.414 9.461 7.161 7.039 2.153 32 228 7.359 .94 70 2260 9420 22 29 42 49 0 6134 68 6066 8.425 6455 6386 .119 10.751 3.075 3.426 3.426
3 1821 1375 273 48 1548 1327 1753 1506 274 52 1480 1458 0 0 980 876 67 18 100 100 100 100 2875 2938 1.167 .857 .985 .692 .98 2.878 12 48 .788 .84 40 2390 9390 21 25 57 61 0 1563 55 1508 .974 1711 1657 1.027 1.119 -.038 .163 .163
4 1140 501 290 56 850 445 1172 533 286 60 882 477 0 0 428 195 69 19 100 100 91 100 1295 1359 1.91 .524 .541 .546 .567 1.503 12 98 .493 .9 50 2550 9400 21 26 72 77 0 569 64 506 .595 606 542 1.681 .615 -.749 -.702 -.702
5 1219 547 261 54 958 493 1233 554 272 57 972 500 0 0 561 321 74 20 93 100 90 93 1451 1472 1.943 .515 .514 .496 .539 1.823 32 176 .47 .87 60 2690 9420 23 29 86 92 0 622 61 560 .585 630 568 1.71 .585 -.774 -.775 -.775
6 802 115 277 55 525 60 816 106 282 57 539 51 0 0 262 50 74 17 93 84 90 59 585 590 8.75 .114 .095 .109 .112 1.676 32 170 .11 .77 60 2840 9410 22 28 101 107 0 131 63 68 .13 120 58 7.7 .108 -2.945 -3.217 -3.217
7 1181 665 282 57 899 608 1234 574 291 59 952 517 0 0 603 487 74 19 96 100 93 100 1507 1469 1.479 .676 .543 .633 .624 1.863 32 176 .682 .9 60 2980 9420 23 29 115 121 0 756 65 691 .769 652 588 1.301 .617 -.38 -.696 -.696
8 806 154 258 56 548 98 847 145 265 58 589 89 0 0 206 44 73 20 100 100 91 100 646 678 5.592 .179 .151 .183 .169 1.834 12 104 .151 .81 50 3130 9420 23 28 130 135 0 175 64 111 .203 165 101 4.921 .172 -2.299 -2.542 -2.542
9 815 158 257 55 558 103 820 146 260 57 563 91 0 0 249 65 65 20 96 92 90 84 661 654 5.417 .185 .162 .158 .189 2.102 52 306 .161 .79 80 3270 9420 22 30 143 151 0 180 63 117 .21 166 103 4.767 .184 -2.253 -2.445 -2.445
10 677 115 239 54 438 61 687 115 243 56 448 61 0 0 131 35 57 18 100 91 100 75 499 509 7.18 .139 .136 .114 .132 2.312 12 104 .085 .61 50 3420 9410 22 27 159 164 0 131 61 69 .158 131 69 6.319 .155 -2.66 -2.692 -2.692
11 1473 420 242 55 1231 365 1473 417 245 56 1231 362 0 0 386 134 59 18 100 100 100 100 1596 1593 3.373 .297 .294 .293 .315 1.535 32 228 .251 .86 70 3550 9410 21 28 171 178 0 477 63 415 .337 474 411 2.968 .334 -1.569 -1.581 -1.581
12 1654 3451 236 57 1418 3394 1428 3096 245 63 1192 3039 0 0 950 2229 78 29 93 100 90 100 4812 4231 .418 2.394 2.549 2.539 2.491 1.966 32 229 2.447 .94 70 3700 9410 21 28 186 193 0 3922 65 3857 2.72 3518 3453 .368 2.897 1.444 1.535 1.535
13 1042 311 244 56 798 255 949 306 255 63 705 250 0 0 423 50 87 28 100 100 100 100 1053 955 3.129 .32 .355 .341 .378 1.571 32 221 .255 .74 70 3840 9410 21 28 200 207 0 353 64 290 .363 348 284 2.754 .403 -1.461 -1.311 -1.311
14 690 128 240 55 450 73 700 129 240 57 460 74 0 0 158 37 56 19 96 90 94 82 523 534 6.164 .162 .161 .142 .144 1.797 52 278 .137 .76 80 3990 9420 22 30 215 223 0 145 63 83 .184 147 84 5.425 .183 -2.44 -2.452 -2.452
15 921 137 227 53 694 84 925 136 230 55 698 83 0 0 197 36 56 18 98 98 98 90 778 781 8.262 .121 .119 .112 .123 1.593 52 246 .109 .81 80 4130 9410 21 29 229 237 0 156 60 95 .138 155 94 7.27 .135 -2.862 -2.888 -2.888
16 2800 5380 227 55 2573 5325 2877 5681 368 57 2650 5626 0 0 1108 1674 2524 18 55 100 0 100 7898 8276 .483 2.07 2.123 2.175 2.117 1.436 52 336 .423 .33 90 4270 9410 20 29 242 251 0 6114 63 6051 2.352 6456 6393 .425 2.413 1.234 1.271 1.271
17 1126 716 220 56 906 660 1119 714 227 58 899 658 0 0 175 131 61 18 100 100 100 100 1566 1557 1.373 .728 .732 .726 .738 1.251 32 213 .695 .94 70 4420 9410 21 28 258 265 0 814 64 750 .828 811 748 1.208 .832 -.273 -.266 -.266
18 281 74 228 57 53 17 236 61 231 59 8 4 0 0 170 58 55 20 34 26 17 13 70 12 3.118 .321 .5 .307 .265 3.801 52 258 .251 .69 80 4560 9410 21 29 272 280 -50 84 65 19 .364 69 5 2.744 .568 -1.456 -.816
19 1307 1886 233 56 1074 1830 1309 1930 238 59 1076 1874 0 0 341 531 53 20 98 100 98 100 2904 2950 .587 1.704 1.742 1.677 1.661 1.331 52 256 1.675 .94 80 4710 9410 21 29 287 295 0 2143 64 2080 1.936 2193 2130 .516 1.979 .953 .985 .985
20 1006 782 225 59 781 723 1015 850 229 60 790 791 0 0 317 307 53 20 98 100 96 100 1504 1581 1.08 .926 1.001 .886 .882 1.49 52 246 .913 .9 80 4860 9410 21 29 302 310 0 889 67 822 1.052 966 899 .951 1.138 .073 .186 .186

Total number of rows: 43104

Table truncated, full table size 9268 Kbytes.




Supplementary data files not provided
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