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Sample GSM90602 Query DataSets for GSM90602
Status Public on Jan 06, 2006
Title ULL-D-201
Sample type RNA
 
Channel 1
Source name Stratagene_aT
Organism Homo sapiens
Characteristics reference: Stratagene Reference, amplified total RNA
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name ULL-D-201_aT
Organism Homo sapiens
Characteristics cell type: primary breast carcinoma
ID: ULL-D-201
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24816.gif
Scanner Make: Axon
name: 24816_Scanner Make
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 04, 2006
Last update date Sep 18, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2790
Series (2)
GSE3971 Invasive lobular and ductal carcinomas of the breast
GSE40954 TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer

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 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
1 4631 1172 162 163 4469 1009 4691 1203 204 191 4529 1040 0 0 1102 210 251 108 100 100 100 100 5478 5569 4.429 .226 .23 .228 .227 1.221 52 337 .22 .96 90 1930 8120 39 48 64 73 0 1247 173 1073 .24 1280 1106 4.163 .244 -2.058 -2.033
2 3129 3272 161 167 2968 3105 3087 3549 193 187 2926 3382 0 0 931 751 206 85 100 100 98 100 6073 6308 .956 1.046 1.156 1.063 1.06 1.238 80 314 1.018 .97 100 2080 8130 40 50 79 89 0 3481 178 3303 1.113 3776 3598 .899 1.23 .154 .298
3 11884 20441 166 165 11718 20276 12513 22372 180 187 12347 22207 0 0 4988 8246 130 113 100 100 100 100 31994 34554 .578 1.73 1.799 1.732 1.713 1.237 120 411 1.725 .98 120 2220 8130 39 51 92 104 0 21746 176 21570 1.841 23800 23624 .543 1.913 .88 .936
4 15372 31095 171 174 15201 30921 16165 31336 197 214 15994 31162 0 0 8043 14536 163 160 100 100 100 100 46122 47156 .492 2.034 1.948 2.142 2.074 1.283 80 302 1.986 .98 100 2370 8140 41 51 108 118 0 33080 185 32895 2.164 33336 33151 .462 2.073 1.114 1.052
5 5829 5066 176 178 5653 4888 6156 5122 207 229 5980 4944 0 0 2791 2098 223 196 100 100 100 100 10541 10924 1.157 .865 .827 .914 .863 1.245 52 288 .829 .98 90 2510 8130 40 49 122 131 0 5389 189 5200 .92 5449 5260 1.087 .88 -.121 -.185
6 1604 1412 176 186 1428 1226 1589 1377 198 236 1413 1191 0 0 342 242 110 167 100 100 100 100 2654 2604 1.165 .859 .843 .865 .874 1.201 52 314 .843 .96 90 2660 8120 39 48 137 146 0 1502 198 1304 .913 1465 1267 1.095 .897 -.131 -.157
7 1603 1325 179 194 1424 1131 1645 1351 213 237 1466 1157 0 0 356 231 137 156 100 100 100 98 2555 2623 1.259 .794 .789 .802 .81 1.224 52 292 .782 .96 90 2800 8120 39 48 151 160 0 1410 206 1203 .845 1437 1231 1.184 .84 -.243 -.252
8 11723 7406 179 184 11544 7222 12664 8293 448 411 12485 8109 0 0 4051 2315 1417 1010 100 100 96 96 18766 20594 1.598 .626 .649 .63 .632 1.229 52 314 .612 .98 90 2940 8120 39 48 165 174 0 7879 196 7683 .666 8822 8627 1.503 .691 -.587 -.533
9 9900 6066 176 174 9724 5892 9878 6370 351 328 9702 6196 0 0 2201 1226 939 684 100 100 100 100 15616 15898 1.65 .606 .639 .607 .621 1.156 52 326 .605 .98 90 3090 8120 39 48 180 189 0 6453 185 6268 .645 6777 6591 1.551 .679 -.634 -.558
10 3547 3572 167 169 3380 3403 3736 3806 204 207 3569 3637 0 0 932 769 290 201 100 100 100 100 6783 7206 .993 1.007 1.019 1.025 1.021 1.167 52 234 .995 .98 80 3240 8130 41 49 196 204 0 3800 180 3620 1.071 4049 3869 .934 1.084 .099 .116
11 22953 16491 165 170 22788 16321 23211 17734 219 239 23046 17564 0 0 4515 3318 383 347 100 100 100 100 39109 40610 1.396 .716 .762 .712 .71 1.167 80 409 .711 .98 110 3380 8130 39 50 208 219 0 17544 181 17363 .762 18866 18685 1.312 .811 -.392 -.303
12 10073 3782 164 172 9909 3610 10287 4014 252 252 10123 3842 0 0 2431 633 523 392 100 100 100 100 13519 13965 2.745 .364 .38 .37 .365 1.2 52 301 .349 .98 90 3530 8130 40 49 224 233 0 4023 183 3840 .388 4270 4087 2.58 .404 -1.367 -1.308
13 7372 5088 157 165 7215 4923 7911 5490 185 193 7754 5325 0 0 2447 1466 182 110 100 100 100 100 12138 13079 1.466 .682 .687 .698 .693 1.189 80 339 .66 .98 100 3680 8140 41 51 239 249 0 5413 176 5237 .726 5840 5665 1.378 .731 -.462 -.453
14 2585 887 163 168 2422 719 2624 900 194 203 2461 732 0 0 466 166 138 111 100 100 100 98 3141 3193 3.369 .297 .297 .293 .282 1.323 52 299 .282 .9 90 3820 8130 40 49 253 262 0 944 179 765 .316 957 779 3.166 .316 -1.663 -1.66
15 12333 7542 169 175 12164 7367 12726 7995 207 216 12557 7820 0 0 3208 1723 276 179 100 100 100 100 19531 20377 1.651 .606 .623 .613 .601 1.165 80 366 .591 .98 100 3970 8140 41 51 268 278 0 8023 186 7837 .644 8505 8319 1.552 .663 -.634 -.594
16 11675 9799 166 172 11509 9627 12352 10652 180 206 12186 10480 0 0 3624 2640 76 155 100 100 100 100 21136 22666 1.195 .836 .86 .857 .846 1.207 80 324 .81 .97 100 4120 8140 41 51 283 293 0 10424 183 10241 .89 11332 11149 1.124 .915 -.168 -.128
17 1916 4961 183 194 1733 4767 1901 5017 210 284 1718 4823 0 0 377 844 151 374 100 100 100 100 6500 6541 .364 2.751 2.807 2.772 2.784 1.171 52 293 2.763 .98 90 4260 8130 40 49 297 306 0 5278 206 5071 2.926 5337 5131 .342 2.987 1.549 1.578
18 806 591 180 191 626 400 760 561 202 235 580 370 0 0 252 127 140 241 100 96 100 17 1026 950 1.565 .639 .638 .644 .636 1.304 52 277 .64 .84 90 4410 8150 42 51 312 321 0 629 203 426 .68 597 394 1.471 .679 -.557 -.559
19 7402 10433 185 195 7217 10238 7420 10499 199 230 7235 10304 0 0 1139 853 90 222 100 100 100 100 17455 17539 .705 1.419 1.424 1.432 1.41 1.164 80 402 1.395 .98 110 4550 8140 40 51 325 336 0 11099 207 10891 1.509 11169 10962 .663 1.515 .594 .599
20 1609 2753 178 186 1431 2567 1572 2809 191 229 1394 2623 0 0 289 407 100 271 100 100 100 100 3998 4017 .557 1.794 1.882 1.806 1.839 1.184 52 212 1.757 .97 80 4700 8140 42 50 342 350 0 2929 198 2731 1.908 2988 2790 .524 2.002 .932 1.001

Total number of rows: 43008

Table truncated, full table size 9898 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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