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Sample GSM90979 Query DataSets for GSM90979
Status Public on Aug 13, 2007
Title BC-M-016
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-016
Organism Homo sapiens
Characteristics BC-M-016
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50743.gif; format: GIF
Datafile type: GenePix Results 3
name: 50743_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
1 723 330 342 169 381 161 762 337 369 177 420 168 0 0 114 52 254 67 82 94 7 71 542 588 2.366 .423 .4 .406 .426 1.441 52 312 .44 .96 90 1440 4540 449 458 139 148 0 464 238 227 .595 474 236 1.682 .563 -.75 -.829 -.829
2 13615 1901 350 172 13265 1729 15012 2072 379 179 14662 1900 0 0 6126 802 242 64 100 100 100 100 14994 16562 7.672 .13 .13 .13 .13 1.228 80 345 .129 .99 100 1580 4540 449 459 153 163 0 2675 242 2433 .183 2916 2674 5.452 .182 -2.447 -2.455 -2.455
3 6817 2624 347 168 6470 2456 7624 2908 357 169 7277 2740 0 0 2763 1060 54 17 100 100 100 100 8926 10017 2.634 .38 .377 .376 .377 1.262 80 350 .378 .99 100 1730 4540 449 459 168 178 0 3692 236 3456 .534 4092 3855 1.872 .53 -.905 -.916 -.916
4 3759 518 330 162 3429 356 4044 527 346 164 3714 365 0 0 1105 122 93 21 100 100 100 100 3785 4079 9.632 .104 .098 .102 .101 1.221 52 281 .106 .96 90 1880 4530 448 457 183 192 0 729 228 501 .146 742 514 6.845 .138 -2.775 -2.854 -2.854
5 1879 466 309 158 1570 308 2094 501 350 164 1785 343 0 0 585 121 237 39 98 100 96 96 1878 2128 5.097 .196 .192 .192 .195 1.345 80 371 .299 .64 100 2020 4540 449 459 197 207 0 656 222 433 .276 705 483 3.623 .27 -1.857 -1.887 -1.887
6 670 280 310 164 360 116 727 290 3524 2952 417 126 0 0 155 66 12193 11395 0 0 0 0 476 543 3.103 .322 .302 .268 .323 1.712 32 192 .695 .97 70 2150 4520 448 455 211 218 0 394 231 163 .453 408 177 2.206 .425 -1.141 -1.234 -1.234
7 2556 659 309 162 2247 497 2747 683 2596 2117 2438 521 0 0 716 157 10341 9653 0 0 0 0 2744 2959 4.521 .221 .214 .225 .227 1.231 52 272 .217 .98 80 2310 4540 450 458 227 235 0 927 228 699 .311 961 733 3.213 .301 -1.684 -1.734 -1.734
8 1302 1144 314 161 988 983 1359 1204 432 199 1045 1043 0 0 310 309 716 271 82 98 3 92 1971 2088 1.005 .995 .998 .995 .991 1.213 80 383 .569 .85 110 2460 4540 448 459 240 251 0 1610 227 1383 1.4 1694 1468 .714 1.404 .485 .49 .49
9 2141 2038 318 164 1823 1874 2183 2097 552 201 1865 1933 0 0 624 412 1563 221 77 100 1 100 3697 3798 .973 1.028 1.036 1.05 1.045 1.216 80 312 .963 .94 100 2600 4540 449 459 255 265 0 2868 231 2637 1.446 2951 2720 .691 1.458 .533 .544 .544
10 2279 2973 313 160 1966 2813 2358 3085 376 172 2045 2925 0 0 554 563 529 83 98 100 93 100 4779 4970 .699 1.431 1.43 1.459 1.477 1.212 80 318 1.419 .96 110 2750 4540 448 459 269 280 0 4183 225 3958 2.013 4341 4116 .497 2.013 1.01 1.009 1.009
11 8958 2319 317 160 8641 2159 9236 2370 483 195 8919 2210 0 0 1788 549 883 187 100 100 100 100 10800 11129 4.002 .25 .248 .245 .249 1.139 80 360 .254 .99 110 2890 4530 447 458 283 294 0 3263 225 3038 .352 3335 3110 2.844 .349 -1.508 -1.52 -1.52
12 7263 5739 294 154 6969 5585 7152 5712 326 162 6858 5558 0 0 2827 2429 171 44 100 100 100 100 12554 12416 1.248 .801 .81 .779 .816 1.333 80 339 .811 .99 100 3040 4540 449 459 299 309 0 8075 217 7859 1.128 8037 7821 .887 1.14 .173 .19 .19
13 3759 2990 246 144 3513 2846 3777 3052 268 147 3531 2908 0 0 746 550 142 37 100 100 100 100 6359 6439 1.234 .81 .824 .818 .814 1.133 80 378 .804 .99 110 3190 4540 448 459 313 324 0 4207 203 4005 1.14 4295 4092 .877 1.159 .189 .213 .213
14 652 289 210 133 442 156 647 290 243 146 437 157 0 0 170 45 277 149 93 60 2 1 598 594 2.833 .353 .359 .353 .358 1.27 80 327 .369 .92 100 3330 4530 448 458 328 338 0 407 187 220 .497 408 221 2.014 .506 -1.01 -.984 -.984
15 858 821 208 132 650 689 861 806 315 157 653 674 0 0 139 207 735 182 25 97 0 92 1339 1327 .943 1.06 1.032 1.018 1.066 1.237 80 334 .296 .59 110 3480 4530 447 458 342 353 0 1155 186 970 1.492 1134 948 .67 1.452 .577 .538 .538
16 6831 4308 199 129 6632 4179 6816 4411 266 141 6617 4282 0 0 1180 985 653 104 100 100 100 100 10811 10899 1.587 .63 .647 .615 .637 1.181 80 369 .636 .97 110 3620 4530 447 458 356 367 0 6062 182 5880 .887 6207 6025 1.128 .911 -.174 -.135 -.135
17 6745 3736 199 131 6546 3605 7188 3747 446 148 6989 3616 0 0 1907 818 2260 122 93 100 88 100 10151 10605 1.816 .551 .517 .576 .561 1.276 80 355 .531 .98 110 3770 4540 448 459 371 382 0 5257 184 5073 .775 5272 5088 1.29 .728 -.368 -.458 -.458
18 3112 2866 194 127 2918 2739 3372 3098 224 136 3178 2971 0 0 660 688 176 64 100 100 100 100 5657 6149 1.065 .939 .935 .927 .936 1.177 80 336 .945 .99 100 3910 4530 448 458 386 396 0 4033 179 3854 1.321 4359 4181 .757 1.315 .401 .396 .396
19 6172 3154 187 127 5985 3027 6260 3106 239 155 6073 2979 0 0 1109 600 300 160 100 100 100 100 9012 9052 1.977 .506 .491 .504 .51 1.105 52 301 .506 .99 90 4050 4530 448 457 400 409 0 4438 179 4259 .712 4370 4192 1.405 .69 -.491 -.535 -.535
20 9341 2983 181 125 9160 2858 9885 3201 257 155 9704 3076 0 0 2761 1031 501 170 100 100 100 98 12018 12780 3.205 .312 .317 .298 .314 1.285 80 368 .316 .99 100 4210 4530 448 458 416 426 0 4197 176 4022 .439 4504 4328 2.278 .446 -1.188 -1.165 -1.165

Total number of rows: 43200

Table truncated, full table size 10006 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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