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Sample GSM90950 Query DataSets for GSM90950
Status Public on Aug 13, 2007
Title BC-M-451
Sample type RNA
 
Channel 1
Source name Stratagene ref aRNA
Organism Homo sapiens
Characteristics Stratagene ref aRNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BC-M-451
Organism Homo sapiens
Characteristics BC-M-451
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50732.gif; format: GIF
Datafile type: GenePix Results 3
name: 50732_Datafile type
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 06, 2006
Last update date Aug 13, 2007
Contact name Therese Sorlie
E-mail(s) tsorlie@labmed.uio.no
Phone +4722934418
Fax +4722934440
Organization name The Norwegian Radium Hospital
Department Genetics
Street address Montebello
City Oslo
ZIP/Postal code 0310
Country Norway
 
Platform ID GPL3319
Series (1)
GSE3985 Micrometastasis primary tumors

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 1105 513 345 175 760 338 1261 542 345 175 916 367 0 0 292 140 27 18 100 100 100 98 1098 1283 2.249 .445 .401 .43 .443 1.28 52 276 .444 .98 80 1120 4150 411 419 108 116 0 563 192 371 .488 595 403 2.049 .44 -1.035 -1.186 -1.186
2 14498 5676 347 175 14151 5501 15496 5909 351 179 15149 5734 0 0 8086 3291 97 92 100 100 100 100 19652 20883 2.572 .389 .379 .375 .399 1.286 80 364 .392 .99 100 1270 4150 410 420 122 132 0 6228 192 6036 .427 6483 6291 2.345 .415 -1.229 -1.268 -1.268
3 13262 9262 338 175 12924 9087 14330 9813 333 173 13992 9638 0 0 6050 4369 32 17 100 100 100 100 22011 23630 1.422 .703 .689 .703 .71 1.245 52 244 .705 .99 80 1410 4150 411 419 137 145 0 10162 192 9970 .771 10767 10575 1.296 .756 -.374 -.404 -.404
4 5224 544 334 170 4890 374 5644 591 332 171 5310 421 0 0 2504 185 30 17 100 98 100 92 5264 5731 13.075 .076 .079 .074 .073 1.382 52 254 .074 .96 80 1550 4150 411 419 151 159 0 597 187 410 .084 648 462 11.917 .087 -3.575 -3.523 -3.523
5 2672 2790 328 171 2344 2619 2805 2812 329 170 2477 2641 0 0 1037 1030 22 15 100 100 100 100 4963 5118 .895 1.117 1.066 1.163 1.099 1.252 52 312 1.093 .98 90 1700 4150 410 419 165 174 0 3061 188 2874 1.226 3085 2898 .816 1.17 .294 .226 .226
6 1072 369 328 170 744 199 1156 390 328 170 828 220 0 0 239 71 20 16 100 100 100 98 943 1048 3.739 .267 .266 .264 .263 1.369 52 267 .267 .95 80 1850 4150 411 419 181 189 0 405 187 218 .293 428 241 3.408 .292 -1.769 -1.778 -1.778
7 2629 2343 324 165 2305 2178 2773 2547 321 165 2449 2382 0 0 1421 1256 30 16 100 100 98 100 4483 4831 1.058 .945 .973 1.006 .936 1.626 52 244 .926 .98 80 1990 4150 411 419 195 203 0 2571 181 2390 1.037 2795 2614 .965 1.067 .052 .094 .094
8 1300 1464 302 165 998 1299 1415 1497 302 165 1113 1332 0 0 440 580 29 17 100 100 100 100 2297 2445 .768 1.302 1.197 1.318 1.281 1.372 80 362 1.314 .96 100 2140 4150 410 420 209 219 0 1606 181 1425 1.428 1642 1461 .7 1.313 .514 .393 .393
9 3433 840 286 156 3147 684 3601 848 286 156 3315 692 0 0 669 208 29 19 100 100 100 100 3831 4007 4.601 .217 .209 .212 .212 1.232 52 277 .212 .97 90 2280 4150 410 419 223 232 0 922 171 750 .238 930 759 4.193 .229 -2.068 -2.126 -2.126
10 2615 4616 279 150 2336 4466 2910 5109 288 155 2631 4959 0 0 930 1728 194 54 100 100 98 100 6802 7590 .523 1.912 1.885 1.937 1.969 1.215 80 342 1.914 .98 100 2430 4150 410 420 238 248 0 5065 165 4900 2.098 5606 5441 .477 2.068 1.069 1.048 1.048
11 17146 22627 316 167 16830 22460 17341 22924 323 181 17025 22757 0 0 2667 3917 111 139 100 100 100 100 39290 39782 .749 1.335 1.337 1.331 1.32 1.07 52 312 1.335 .99 90 2570 4140 409 418 252 261 0 24826 183 24643 1.464 25152 24969 .683 1.467 .55 .552 .552
12 13379 26767 321 171 13058 26596 14267 29318 332 184 13946 29147 0 0 4460 7960 106 138 100 100 100 100 39654 43093 .491 2.037 2.09 2.111 2.012 1.196 52 312 2.002 .99 90 2720 4150 410 419 267 276 0 29368 188 29181 2.235 32167 31980 .447 2.293 1.16 1.197 1.197
13 9950 9152 308 167 9642 8985 10542 10058 324 171 10234 9891 0 0 2692 3018 180 43 100 100 100 100 18627 20125 1.073 .932 .966 .898 .95 1.197 52 312 .958 .99 90 2870 4140 409 418 282 291 0 10041 183 9858 1.022 11036 10852 .978 1.06 .032 .085 .085
14 1165 1649 312 169 853 1480 1168 1693 326 173 856 1524 0 0 166 220 180 42 100 100 100 100 2333 2380 .576 1.735 1.78 1.748 1.745 1.137 52 312 1.427 .73 90 3010 4140 409 418 296 305 0 1809 185 1624 1.904 1858 1672 .525 1.953 .929 .966 .966
15 2271 2777 305 165 1966 2612 2297 2819 306 166 1992 2654 0 0 251 366 24 18 100 100 100 100 4578 4646 .753 1.329 1.332 1.325 1.321 1.07 52 289 1.358 .99 90 3160 4140 409 418 311 320 0 3047 181 2866 1.458 3093 2912 .686 1.462 .544 .548 .548
16 16469 22603 302 168 16167 22435 19576 26309 334 174 19274 26141 0 0 7110 9711 351 60 100 100 98 100 38602 45415 .721 1.388 1.356 1.426 1.388 1.273 80 362 1.387 .99 100 3310 4150 410 420 326 336 0 24800 184 24615 1.523 28866 28682 .657 1.488 .607 .573 .573
17 14366 8311 313 176 14053 8135 14759 8531 971 602 14446 8355 0 0 3548 2495 4757 2836 100 94 88 84 22188 22801 1.727 .579 .578 .559 .586 1.237 52 300 .62 .95 90 3450 4140 409 418 340 349 0 9119 193 8926 .635 9360 9167 1.574 .635 -.655 -.656 -.656
18 4691 10708 317 186 4374 10522 4691 12401 1417 776 4374 12215 0 0 2962 4267 5301 3019 17 90 1 80 14896 16589 .416 2.406 2.793 2.405 2.676 1.336 52 273 2.327 .87 80 3600 4150 411 419 356 364 0 11749 204 11545 2.639 13606 13402 .379 3.064 1.4 1.615 1.615
19 11253 8283 303 172 10950 8111 12653 9729 563 222 12350 9557 0 0 5309 4049 1465 300 96 100 84 100 19061 21907 1.35 .741 .774 .725 .729 1.183 52 311 .736 .97 90 3760 4140 409 418 371 380 0 9088 189 8899 .813 10675 10486 1.23 .849 -.299 -.236 -.236
20 17403 17390 326 180 17077 17210 18117 18711 850 377 17791 18531 0 0 5370 6919 3359 1286 100 100 96 100 34287 36322 .992 1.008 1.042 .957 1.013 1.213 52 288 1.057 .99 90 3890 4140 409 418 384 393 0 19080 197 18883 1.106 20530 20332 .904 1.143 .145 .193 .193

Total number of rows: 43200

Table truncated, full table size 10143 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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