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Sample GSM91918 Query DataSets for GSM91918
Status Public on Jan 12, 2006
Title LAPC4vsCRG
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 LAPC4 total RNA
Organism Homo sapiens
Characteristics LAPC4 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35462.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 1099 212 85 84 1014 128 1079 201 109 89 994 117 0 0 299 87 77 38 100 87 100 71 1142 1111 7.922 .126 .118 .113 .128 2.293 32 148 .114 .7 60 1720 9330 42 48 25 31 0 221 88 133 .131 209 122 7.605 .123 -2.927 -3.028 -3.028
2 3705 13156 113 101 3592 13055 3971 14182 178 136 3858 14081 0 0 1321 3833 152 235 96 100 96 100 16647 17939 .275 3.634 3.65 3.871 3.672 1.559 52 316 3.692 .97 90 1870 9330 40 49 38 47 0 13704 105 13599 3.786 14773 14668 .264 3.802 1.921 1.927 1.927
3 2955 2358 292 120 2663 2238 2822 2341 349 216 2530 2221 0 0 1512 1096 272 331 90 96 90 93 4901 4751 1.19 .84 .878 .964 .819 1.926 32 167 .781 .94 60 2010 9320 41 47 54 60 0 2456 125 2331 .875 2439 2314 1.142 .914 -.192 -.129 -.129
4 1570 1031 269 105 1301 926 1593 993 288 139 1324 888 0 0 423 284 185 115 100 100 93 96 2227 2212 1.405 .712 .671 .72 .732 1.368 32 165 .646 .92 60 2160 9320 41 47 69 75 0 1074 109 965 .741 1034 925 1.349 .699 -.432 -.517 -.517
5 2305 2444 182 102 2123 2342 2213 2573 223 123 2031 2471 0 0 801 767 177 91 100 100 100 100 4465 4502 .906 1.103 1.217 1.119 1.103 1.372 52 288 1.059 .93 80 2300 9320 40 48 82 90 0 2546 106 2440 1.149 2680 2574 .87 1.267 .201 .342 .342
6 1167 270 288 123 879 147 1128 268 314 133 840 145 0 0 288 69 262 62 91 91 91 66 1026 985 5.98 .167 .173 .19 .181 1.771 12 104 .122 .59 50 2440 9320 41 46 97 102 0 281 128 153 .174 279 151 5.74 .18 -2.521 -2.475 -2.475
7 2854 2266 572 160 2282 2106 2936 2287 607 201 2364 2127 0 0 658 630 284 234 100 100 100 100 4388 4491 1.084 .923 .9 .923 .984 1.318 32 232 .907 .91 70 2590 9320 40 47 111 118 0 2360 167 2194 .961 2382 2216 1.04 .937 -.057 -.094 -.094
8 1943 389 568 170 1375 219 1981 360 586 194 1413 190 0 0 478 110 221 200 96 43 96 3 1594 1603 6.279 .159 .134 .154 .147 2.073 32 219 .15 .77 70 2740 9320 40 47 126 133 0 405 177 228 .166 375 198 6.027 .14 -2.592 -2.836 -2.836
9 1798 398 455 148 1343 250 1760 381 489 157 1305 233 0 0 295 103 353 72 100 96 100 86 1593 1538 5.372 .186 .179 .172 .184 1.669 52 337 .177 .81 90 2890 9320 39 48 140 149 0 415 154 260 .194 397 243 5.157 .186 -2.367 -2.427 -2.427
10 806 659 340 129 466 530 833 674 378 137 493 545 0 0 211 193 146 53 93 100 81 100 996 1038 .879 1.137 1.105 1.352 1.058 2.44 32 158 1.082 .75 60 3040 9320 41 47 157 163 0 686 134 552 1.185 702 568 .844 1.152 .245 .204 .204
11 4777 678 279 117 4498 561 4910 684 331 144 4631 567 0 0 1203 221 408 158 100 94 98 86 5059 5198 8.018 .125 .122 .118 .127 1.504 52 338 .116 .92 90 3180 9320 39 48 169 178 0 706 122 584 .13 713 591 7.697 .128 -2.944 -2.971 -2.971
12 5415 10572 271 127 5144 10445 5501 10691 331 222 5230 10564 0 0 2352 3622 410 454 96 100 96 100 15589 15794 .492 2.031 2.02 2.227 2.035 1.573 32 212 1.845 .95 70 3330 9310 39 46 185 192 0 11013 132 10880 2.115 11136 11004 .473 2.104 1.081 1.073 1.073
13 1684 1971 245 117 1439 1854 1760 1964 266 153 1515 1847 0 0 503 576 115 305 98 100 97 100 3293 3362 .776 1.288 1.219 1.34 1.24 1.482 80 403 1.389 .9 110 3470 9330 39 50 197 208 0 2053 122 1931 1.342 2046 1924 .745 1.27 .424 .345 .345
14 800 231 245 118 555 113 792 222 256 124 547 104 0 0 164 78 77 50 100 76 100 52 668 651 4.912 .204 .19 .186 .202 2.019 80 333 .19 .63 100 3620 9330 40 50 213 223 0 241 123 118 .212 231 108 4.715 .198 -2.237 -2.336 -2.336
15 1827 381 281 126 1546 255 1855 377 290 137 1574 251 0 0 390 116 90 70 100 96 98 86 1801 1825 6.063 .165 .159 .161 .161 1.77 52 265 .162 .77 90 3770 9320 39 48 228 237 0 397 131 266 .172 393 261 5.82 .166 -2.541 -2.59 -2.59
16 7704 12712 270 129 7434 12583 8321 13792 285 146 8051 13663 0 0 3027 4199 111 80 97 100 97 100 20017 21714 .591 1.693 1.697 1.878 1.702 1.955 80 342 1.651 .97 100 3910 9330 40 50 242 252 0 13242 134 13107 1.763 14367 14232 .567 1.768 .818 .822 .822
17 2687 2399 216 111 2471 2288 2586 2383 239 121 2370 2272 0 0 909 635 277 77 100 100 100 100 4759 4642 1.08 .926 .959 .936 .917 1.31 52 289 .879 .93 90 4060 9320 39 48 257 266 0 2499 116 2383 .965 2482 2367 1.037 .999 -.052 -.002 -.002
18 324 127 211 106 113 21 274 115 376 116 63 9 0 0 150 48 2052 80 0 13 0 0 134 72 5.381 .186 .143 .399 .515 4.686 52 245 .005 .14 80 4210 9310 39 47 273 281 -50 132 110 22 .194 120 9 5.166 .149 -2.369 -2.748
19 3592 7464 232 114 3360 7350 3666 7990 344 121 3434 7876 0 0 1097 2196 1679 64 91 100 56 100 10710 11310 .457 2.188 2.294 2.236 2.201 1.348 80 362 1.772 .6 100 4350 9320 39 49 286 296 0 7775 119 7656 2.279 8323 8204 .439 2.389 1.188 1.256 1.256
20 2455 2377 240 119 2215 2258 2455 2354 258 123 2215 2235 0 0 687 505 186 46 100 100 100 100 4473 4450 .981 1.019 1.009 1.049 1.047 1.268 52 276 .341 .49 90 4500 9320 39 48 301 310 0 2476 124 2352 1.062 2452 2328 .942 1.051 .087 .072 .072

Total number of rows: 43104

Table truncated, full table size 9760 Kbytes.




Supplementary data files not provided
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