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Sample GSM90955 Query DataSets for GSM90955
Status Public on Aug 13, 2007
Title BC-M-101
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-101
Organism Homo sapiens
Characteristics BC-M-101
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49760.gif; format: GIF
Datafile type: GenePix Results 3
name: 49760_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
1 319 344 85 126 234 218 321 352 87 128 236 226 0 0 61 74 16 22 100 100 100 98 452 462 1.073 .932 .958 .9 .93 1.464 52 245 .977 .93 80 1480 8600 856 864 144 152 0 581 213 368 1.573 594 382 .636 1.617 .653 .693 .693
2 2936 738 85 121 2851 617 3013 716 88 124 2928 595 0 0 706 173 15 21 100 100 100 100 3468 3523 4.621 .216 .203 .214 .217 1.227 52 244 .213 .98 80 1620 8600 856 864 158 166 0 1246 204 1042 .365 1209 1005 2.737 .343 -1.453 -1.543 -1.543
3 885 509 85 119 800 390 870 530 90 127 785 411 0 0 593 203 22 37 100 96 98 94 1190 1196 2.051 .488 .524 .532 .571 1.75 52 243 .379 .83 80 1770 8600 856 864 173 181 0 859 201 658 .823 895 694 1.215 .884 -.281 -.178 -.178
4 514 314 89 127 425 187 534 304 94 135 445 177 0 0 181 111 29 40 100 90 100 82 612 622 2.273 .44 .398 .382 .417 1.642 52 244 .458 .91 80 1910 8600 856 864 187 195 0 530 214 316 .743 513 299 1.346 .672 -.429 -.575 -.575
5 8079 4280 92 129 7987 4151 9084 4310 127 140 8992 4181 0 0 3370 1905 262 54 100 100 100 100 12138 13173 1.924 .52 .465 .511 .539 1.221 52 301 .518 .98 90 2050 8600 855 864 200 209 0 7226 218 7008 .877 7276 7059 1.14 .785 -.189 -.349 -.349
6 619 395 93 125 526 270 654 409 130 135 561 284 0 0 176 94 286 55 90 100 48 92 796 845 1.948 .513 .506 .512 .514 1.287 52 251 .503 .96 80 2210 8600 856 864 217 225 0 667 211 456 .867 691 479 1.154 .855 -.207 -.227 -.227
7 5936 2313 94 121 5842 2192 5993 2594 95 123 5899 2473 0 0 2285 865 18 20 100 100 100 100 8034 8372 2.665 .375 .419 .371 .369 1.214 52 255 .37 .98 80 2350 8600 856 864 231 239 0 3905 204 3701 .633 4379 4175 1.579 .708 -.659 -.499 -.499
8 1018 1657 87 114 931 1543 1017 1492 88 114 930 1378 0 0 287 556 13 18 100 100 100 100 2474 2308 .603 1.657 1.482 1.625 1.72 1.255 52 243 1.734 .96 80 2500 8600 856 864 246 254 0 2797 192 2605 2.798 2519 2326 .357 2.502 1.484 1.323 1.323
9 2604 616 85 120 2519 496 2712 633 87 121 2627 513 0 0 765 158 18 17 100 100 100 100 3015 3140 5.079 .197 .195 .195 .196 1.231 80 331 .193 .98 100 2650 8600 855 865 260 270 0 1040 203 837 .332 1069 866 3.008 .33 -1.589 -1.601 -1.601
10 1114 899 84 110 1030 789 1153 869 87 112 1069 759 0 0 327 257 21 20 100 100 100 100 1819 1828 1.305 .766 .71 .768 .76 1.488 52 209 .761 .93 80 2790 8600 856 864 275 283 0 1518 186 1332 1.293 1467 1281 .773 1.199 .371 .261 .261
11 5850 9452 81 113 5769 9339 6077 9989 152 224 5996 9876 0 0 1632 2577 485 783 100 100 100 100 15108 15872 .618 1.619 1.647 1.624 1.508 1.191 52 293 1.599 .98 90 2920 8600 855 864 287 296 0 15958 191 15767 2.733 16864 16673 .366 2.781 1.45 1.475 1.475
12 7713 6540 84 119 7629 6421 7792 6525 152 223 7708 6406 0 0 3071 2500 471 759 100 100 96 96 14050 14114 1.188 .842 .831 .876 .837 1.325 52 311 .838 .98 90 3080 8600 855 864 303 312 0 11041 201 10840 1.421 11016 10815 .704 1.403 .507 .489 .489
13 9551 4022 86 120 9465 3902 9325 3771 90 124 9239 3651 0 0 2911 1277 27 24 100 100 100 100 13367 12890 2.426 .412 .395 .41 .413 1.162 80 345 .412 .99 100 3230 8600 855 865 318 328 0 6790 203 6588 .696 6366 6164 1.437 .667 -.523 -.584 -.584
14 872 724 87 120 785 604 847 688 90 123 760 568 0 0 290 277 23 23 100 100 100 100 1389 1328 1.3 .769 .747 .741 .757 1.285 80 329 .798 .97 100 3380 8600 855 865 333 343 0 1222 203 1020 1.299 1162 959 .77 1.262 .377 .335 .335
15 1653 2013 90 122 1563 1891 1776 2043 92 122 1686 1921 0 0 421 535 16 15 100 100 100 100 3454 3607 .827 1.21 1.139 1.213 1.19 1.271 80 301 1.223 .98 100 3530 8600 855 865 348 358 0 3398 206 3193 2.043 3449 3243 .49 1.924 1.03 .944 .944
16 6127 5729 89 117 6038 5612 6456 5900 91 119 6367 5783 0 0 1591 1330 17 17 100 100 100 100 11650 12150 1.076 .929 .908 .944 .927 1.202 80 321 .921 .99 100 3670 8600 855 865 362 372 0 9672 198 9475 1.569 9961 9763 .637 1.533 .65 .617 .617
17 8552 4813 81 115 8471 4698 8539 4701 83 117 8458 4586 0 0 1767 1006 16 16 100 100 100 100 13169 13044 1.803 .555 .542 .554 .557 1.125 52 241 .55 .99 80 3810 8600 856 864 377 385 0 8126 194 7931 .936 7937 7742 1.068 .915 -.095 -.128 -.128
18 209 210 74 111 135 99 114 129 76 111 40 18 0 0 200 174 13 15 98 55 86 36 234 58 1.364 .733 .45 .511 .542 2.588 52 239 .91 .95 80 3970 8590 855 863 393 401 -50 355 187 167 1.238 218 30 .808 .76 .308 -.396
19 9651 7794 83 113 9568 7681 9940 8341 83 116 9857 8228 0 0 3375 2687 16 20 100 100 100 100 17249 18085 1.246 .803 .835 .81 .807 1.149 80 316 .803 .99 100 4100 8600 855 865 405 415 0 13158 191 12968 1.355 14082 13891 .738 1.409 .439 .495 .495
20 12516 7107 87 118 12429 6989 13406 7596 134 154 13319 7478 0 0 3832 2318 322 264 100 100 100 100 19418 20797 1.778 .562 .561 .552 .559 1.172 52 303 .565 .99 90 4250 8590 854 863 420 429 0 11999 199 11799 .949 12824 12625 1.053 .948 -.075 -.077 -.077

Total number of rows: 43104

Table truncated, full table size 9877 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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