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Sample GSM90989 Query DataSets for GSM90989
Status Public on Aug 13, 2007
Title BC-M-275
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-275
Organism Homo sapiens
Characteristics BC-M-275
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49774.gif; format: GIF
Datafile type: GenePix Results 3
name: 49774_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 GPL3315
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
1 194 299 70 100 124 199 198 318 71 102 128 218 0 0 51 92 13 14 98 96 96 96 323 346 .623 1.605 1.703 1.522 1.634 1.384 52 256 1.7 .93 80 1300 8610 857 865 126 134 0 668 223 444 3.584 710 487 .279 3.804 1.842 1.928 1.928
2 6897 969 69 103 6828 866 6719 959 71 110 6650 856 0 0 2475 298 15 29 100 100 100 100 7694 7506 7.885 .127 .129 .128 .129 1.158 52 313 .123 .98 90 1440 8600 855 864 139 148 0 2164 230 1934 .283 2142 1912 3.53 .288 -1.82 -1.798 -1.798
3 652 526 68 101 584 425 599 507 69 103 531 406 0 0 237 154 10 17 100 100 100 100 1009 937 1.374 .728 .765 .759 .717 1.402 32 212 .71 .96 70 1590 8600 856 863 155 162 0 1175 226 949 1.625 1132 907 .615 1.708 .701 .772 .772
4 579 268 69 99 510 169 609 291 69 103 540 192 0 0 247 92 9 29 100 90 100 80 679 732 3.018 .331 .356 .288 .332 1.913 52 252 .328 .94 80 1740 8600 856 864 170 178 0 599 221 377 .74 650 429 1.351 .794 -.434 -.333 -.333
5 3237 1542 71 96 3166 1446 3077 1567 72 98 3006 1471 0 0 1392 677 13 14 100 100 100 100 4612 4477 2.189 .457 .489 .454 .475 1.251 52 309 .461 .97 90 1870 8600 855 864 182 191 0 3444 214 3230 1.02 3500 3286 .98 1.093 .029 .128 .128
6 274 292 72 95 202 197 277 287 74 97 205 192 0 0 43 48 14 13 100 100 100 100 399 397 1.025 .975 .937 .966 .941 1.207 32 212 .985 .95 70 2030 8600 856 863 199 206 0 652 212 440 2.178 641 429 .459 2.092 1.123 1.065 1.065
7 2249 921 73 95 2176 826 2200 932 75 101 2127 837 0 0 873 342 12 54 100 100 100 100 3002 2964 2.634 .38 .394 .377 .377 1.276 52 286 .37 .96 80 2170 8600 856 864 213 221 0 2057 212 1845 .848 2082 1869 1.179 .879 -.238 -.186 -.186
8 205 359 73 95 132 264 203 347 74 99 130 252 0 0 33 72 11 17 100 100 100 100 396 382 .5 2 1.938 1.98 1.997 1.239 32 206 2.016 .93 70 2320 8600 856 863 228 235 0 802 212 590 4.467 775 563 .224 4.33 2.159 2.114 2.114
9 1473 337 73 98 1400 239 1515 333 74 100 1442 235 0 0 316 61 11 15 100 100 100 100 1639 1677 5.858 .171 .163 .17 .174 1.235 52 327 .169 .96 90 2460 8600 855 864 241 250 0 753 219 534 .381 744 525 2.623 .364 -1.391 -1.458 -1.458
10 236 340 75 100 161 240 238 351 76 102 163 251 0 0 64 78 10 15 100 100 100 100 401 414 .671 1.491 1.54 1.537 1.537 1.319 52 250 1.455 .94 80 2620 8600 856 864 258 266 0 759 223 536 3.329 784 561 .3 3.439 1.735 1.782 1.782
11 2261 3005 71 100 2190 2905 2316 3015 73 101 2245 2915 0 0 747 993 11 14 100 100 100 100 5095 5160 .754 1.326 1.298 1.332 1.323 1.154 52 310 1.341 .99 90 2750 8600 855 864 270 279 0 6712 223 6488 2.963 6734 6511 .338 2.9 1.567 1.536 1.536
12 2805 2772 71 100 2734 2672 2809 2790 72 101 2738 2690 0 0 1308 1300 11 17 100 100 100 100 5406 5428 1.023 .977 .982 .977 .98 1.472 52 262 .974 .97 80 2910 8600 856 864 287 295 0 6191 223 5968 2.183 6232 6008 .458 2.194 1.126 1.134 1.134
13 4323 2076 71 94 4252 1982 4115 1998 72 96 4044 1904 0 0 2004 1124 10 15 100 100 100 100 6234 5948 2.145 .466 .471 .454 .459 1.166 80 402 .482 .98 110 3060 8600 854 865 300 311 0 4637 210 4427 1.041 4463 4253 .961 1.052 .058 .073 .073
14 260 276 74 97 186 179 255 276 75 99 181 179 0 0 66 54 11 16 100 100 98 100 365 360 1.039 .962 .989 .987 .97 1.366 80 315 .945 .93 100 3200 8600 855 865 315 325 0 616 217 400 2.149 616 400 .465 2.209 1.104 1.143 1.143
15 604 582 76 100 528 482 643 605 77 102 567 505 0 0 169 167 12 14 100 100 100 100 1010 1072 1.095 .913 .891 .901 .913 1.277 80 313 .919 .98 100 3340 8600 855 865 329 339 0 1300 223 1077 2.039 1351 1128 .49 1.989 1.028 .992 .992
16 2886 2621 74 98 2812 2523 2908 2571 75 100 2834 2473 0 0 1118 1048 11 14 100 100 100 100 5335 5307 1.115 .897 .873 .889 .891 1.225 80 356 .903 .99 100 3490 8600 855 865 344 354 0 5854 219 5635 2.004 5742 5523 .499 1.949 1.003 .963 .963
17 3337 1370 72 96 3265 1274 3412 1405 74 99 3340 1309 0 0 733 356 23 16 100 100 100 100 4539 4649 2.563 .39 .392 .384 .391 1.191 52 276 .392 .98 90 3630 8600 855 864 358 367 0 3060 214 2846 .872 3138 2924 1.147 .875 -.198 -.192 -.192
18 115 123 69 91 46 32 77 97 74 94 8 6 0 0 84 62 44 28 21 23 21 19 78 14 1.438 .696 .75 .951 .758 3.363 52 245 .57 .94 80 3780 8590 855 863 374 382 -50 275 203 71 1.554 217 13 .644 1.675 .636 .744
19 3655 2111 72 95 3583 2016 3782 2293 76 100 3710 2198 0 0 1620 953 37 28 100 100 100 100 5599 5908 1.777 .563 .592 .543 .566 1.299 80 345 .565 .99 100 3920 8600 855 865 387 397 0 4715 212 4503 1.257 5121 4909 .796 1.323 .33 .404 .404
20 4177 2256 74 99 4103 2157 4364 2217 75 100 4290 2118 0 0 2002 1113 9 14 100 100 100 100 6260 6408 1.902 .526 .494 .507 .521 1.383 80 353 .529 .99 100 4070 8600 855 865 402 412 0 5039 221 4818 1.174 4952 4731 .852 1.103 .232 .141 .141

Total number of rows: 43104

Table truncated, full table size 9534 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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