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Sample GSM90973 Query DataSets for GSM90973
Status Public on Aug 13, 2007
Title BC-M-245
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-245
Organism Homo sapiens
Characteristics BC-M-245
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49769.gif; format: GIF
Datafile type: GenePix Results 3
name: 49769_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
1 232 293 68 97 164 196 246 307 68 98 178 210 0 0 45 71 10 12 100 98 98 98 360 388 .837 1.195 1.18 1.147 1.16 1.3 52 254 1.261 .96 80 1390 8770 873 881 135 143 0 618 205 413 2.52 647 443 .397 2.488 1.334 1.315 1.315
2 8809 1524 68 96 8741 1428 9150 1596 70 99 9082 1500 0 0 3744 641 12 25 100 100 100 100 10169 10582 6.121 .163 .165 .156 .168 1.285 52 302 .163 .98 90 1520 8760 871 880 147 156 0 3214 202 3012 .345 3366 3163 2.902 .348 -1.537 -1.522 -1.522
3 880 526 73 97 807 429 859 496 75 100 786 399 0 0 290 170 15 16 100 100 100 100 1236 1185 1.881 .532 .508 .521 .524 1.223 32 212 .536 .97 70 1670 8760 872 879 163 170 0 1109 205 905 1.121 1046 841 .892 1.071 .165 .098 .098
4 757 247 70 96 687 151 784 251 71 97 714 155 0 0 273 58 12 13 100 100 100 98 838 869 4.55 .22 .217 .221 .219 1.412 52 252 .21 .95 80 1820 8760 872 880 178 186 0 521 202 318 .464 529 327 2.157 .458 -1.109 -1.127 -1.127
5 4242 977 69 98 4173 879 4610 1086 75 102 4541 988 0 0 1986 430 45 18 100 100 100 100 5052 5529 4.747 .211 .218 .21 .215 1.273 52 300 .211 .98 90 1950 8760 871 880 190 199 0 2060 207 1854 .444 2290 2084 2.251 .459 -1.171 -1.124 -1.124
6 330 270 70 100 260 170 344 271 80 117 274 171 0 0 81 61 58 138 98 69 92 5 430 445 1.529 .654 .624 .652 .665 1.306 52 262 .676 .96 80 2110 8760 872 880 207 215 0 569 211 359 1.379 572 361 .725 1.316 .464 .396 .396
7 2450 763 72 101 2378 662 2320 769 74 101 2248 668 0 0 1039 314 10 13 100 100 100 100 3040 2916 3.592 .278 .297 .274 .277 1.302 52 312 .273 .97 90 2250 8760 871 880 220 229 0 1609 213 1396 .587 1622 1409 1.703 .627 -.768 -.674 -.674
8 287 300 73 100 214 200 295 313 74 100 222 213 0 0 53 72 11 11 100 100 100 100 414 435 1.07 .935 .959 .887 .896 1.355 52 312 .996 .95 90 2400 8760 871 880 235 244 0 633 211 422 1.971 660 449 .507 2.023 .979 1.017 1.017
9 1468 311 72 102 1396 209 1502 325 75 102 1430 223 0 0 367 67 21 11 100 100 100 100 1605 1653 6.679 .15 .156 .145 .15 1.296 52 311 .144 .96 90 2540 8760 871 880 249 258 0 656 215 441 .316 685 470 3.167 .329 -1.663 -1.604 -1.604
10 363 237 71 101 292 136 365 232 75 102 294 131 0 0 81 47 23 12 100 100 100 100 428 425 2.147 .466 .446 .457 .467 1.378 52 250 .472 .94 80 2700 8760 872 880 266 274 0 500 213 287 .982 489 276 1.018 .94 -.026 -.09 -.09
11 4434 556 72 100 4362 456 4605 565 79 101 4533 465 0 0 1493 159 44 12 100 100 100 100 4818 4998 9.566 .105 .103 .105 .108 1.238 52 301 .102 .97 90 2830 8760 871 880 278 287 0 1173 211 962 .22 1192 981 4.536 .216 -2.181 -2.209 -2.209
12 4045 3381 72 98 3973 3283 4178 3432 82 102 4106 3334 0 0 1654 1377 50 24 100 100 100 100 7256 7440 1.21 .826 .812 .828 .825 1.272 52 275 .823 .98 80 2980 8760 872 880 294 302 0 7130 207 6924 1.743 7238 7031 .574 1.712 .801 .776 .776
13 4057 2795 73 97 3984 2698 3785 2635 76 100 3712 2538 0 0 1458 1139 20 21 100 100 100 100 6682 6250 1.477 .677 .684 .658 .678 1.218 80 419 .692 .99 110 3140 8760 870 881 308 319 0 5894 205 5690 1.428 5557 5352 .7 1.442 .514 .528 .528
14 357 312 69 96 288 216 360 317 70 97 291 221 0 0 90 79 10 13 100 100 100 100 504 512 1.333 .75 .759 .727 .758 1.289 80 321 .769 .97 100 3280 8760 871 881 323 333 0 658 202 456 1.582 669 466 .632 1.602 .661 .68 .68
15 926 523 71 99 855 424 1026 555 73 101 955 456 0 0 294 163 12 14 100 100 100 100 1279 1411 2.017 .496 .477 .482 .502 1.318 80 323 .501 .98 100 3420 8760 871 881 337 347 0 1103 209 894 1.046 1170 962 .956 1.007 .065 .01 .01
16 4570 3555 71 100 4499 3455 4662 3747 72 101 4591 3647 0 0 1857 1450 12 12 100 100 100 100 7954 8238 1.302 .768 .794 .757 .782 1.273 80 378 .768 .99 100 3570 8760 871 881 352 362 0 7497 211 7286 1.62 7902 7691 .617 1.675 .696 .744 .744
17 4745 1651 67 98 4678 1553 4282 1630 68 100 4215 1532 0 0 1616 402 10 13 100 100 100 100 6231 5747 3.012 .332 .363 .337 .341 1.174 52 289 .319 .98 90 3720 8760 871 880 367 376 0 3482 207 3275 .7 3438 3231 1.428 .767 -.514 -.384 -.384
18 166 154 67 98 99 56 96 118 68 99 29 20 0 0 133 82 9 11 90 65 69 42 155 49 1.768 .566 .69 .629 .577 1.983 52 246 .587 .9 80 3860 8750 871 879 382 390 -50 325 207 118 1.193 249 42 .838 1.454 .255 .54
19 6099 3607 72 100 6027 3507 6125 3586 76 108 6053 3486 0 0 1412 789 23 64 100 100 100 100 9534 9539 1.719 .582 .576 .584 .583 1.154 52 302 .582 .98 90 4000 8760 871 880 395 404 0 7607 211 7396 1.227 7563 7352 .815 1.215 .295 .28 .28
20 5037 2574 73 99 4964 2475 5211 2600 76 102 5138 2501 0 0 2004 1050 16 15 100 100 100 100 7439 7639 2.006 .499 .487 .479 .497 1.316 80 385 .499 .99 100 4160 8760 871 881 411 421 0 5428 209 5220 1.051 5483 5274 .951 1.027 .072 .038 .038

Total number of rows: 43104

Table truncated, full table size 9659 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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