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Sample GSM90556 Query DataSets for GSM90556
Status Public on Jan 06, 2006
Title ULL-D-087
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-087_aT
Organism Homo sapiens
Characteristics cell type: primary breast carcinoma
ID: ULL-D-087
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/2002-01/24803.gif
Scanner Make: Axon
name: 24803_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 2616 1159 156 145 2460 1014 2661 1233 171 153 2505 1088 0 0 660 283 95 56 100 100 100 100 3474 3593 2.426 .412 .434 .406 .424 1.252 52 329 .411 .97 90 1850 7910 38 47 48 57 0 1136 142 994 .404 1209 1067 2.475 .426 -1.307 -1.232
2 2381 1085 153 146 2228 939 2395 1100 162 151 2242 954 0 0 744 312 64 46 100 100 100 100 3167 3196 2.373 .421 .426 .417 .411 1.257 80 333 .411 .97 100 2000 7920 39 49 63 73 0 1064 143 921 .413 1078 935 2.42 .417 -1.275 -1.261
3 6772 11078 153 141 6619 10937 7251 11973 158 149 7098 11832 0 0 2764 4021 35 54 100 100 99 100 17556 18930 .605 1.652 1.667 1.772 1.654 1.488 120 474 1.618 .98 130 2150 7930 38 51 76 89 0 10861 138 10723 1.62 11738 11600 .617 1.634 .696 .709
4 16375 30684 162 144 16213 30540 17152 33089 168 157 16990 32945 0 0 4392 8611 36 68 100 100 100 100 46753 49935 .531 1.884 1.939 1.865 1.876 1.184 52 268 1.897 .98 90 2290 7920 39 48 92 101 0 30082 141 29941 1.847 32440 32299 .541 1.901 .885 .927
5 4116 2329 166 148 3950 2181 4079 2494 174 157 3913 2346 0 0 1672 929 52 51 100 100 100 100 6131 6259 1.811 .552 .6 .539 .544 1.237 52 288 .549 .98 90 2440 7910 38 47 107 116 0 2283 145 2138 .541 2445 2300 1.847 .588 -.885 -.767
6 1062 1031 166 150 896 881 1086 1027 170 158 920 877 0 0 221 173 32 44 100 100 100 100 1777 1797 1.017 .983 .953 .998 .983 1.239 52 292 .958 .96 90 2580 7910 38 47 121 130 0 1011 147 864 .964 1007 860 1.037 .935 -.053 -.098
7 1335 1446 160 144 1175 1302 1343 1484 162 155 1183 1340 0 0 297 232 31 65 100 100 100 100 2477 2523 .902 1.108 1.133 1.129 1.125 1.204 52 293 1.084 .97 90 2720 7910 38 47 135 144 0 1418 141 1276 1.086 1455 1314 .921 1.111 .119 .151
8 10087 7154 154 139 9933 7015 10634 7762 158 147 10480 7623 0 0 3867 2415 29 49 100 100 100 100 16948 18103 1.416 .706 .727 .716 .7 1.255 80 349 .684 .98 100 2870 7920 39 49 150 160 0 7014 136 6877 .692 7610 7474 1.444 .713 -.53 -.488
9 4711 5231 158 146 4553 5085 4880 5402 160 147 4722 5256 0 0 1661 1723 29 28 100 100 100 100 9638 9978 .895 1.117 1.113 1.138 1.108 1.241 80 323 1.103 .97 100 3020 7920 39 49 165 175 0 5128 143 4985 1.095 5296 5153 .913 1.091 .131 .126
10 1836 4984 166 153 1670 4831 1928 5169 167 153 1762 5016 0 0 532 1314 30 27 100 100 100 100 6501 6778 .346 2.893 2.847 2.959 2.877 1.249 52 246 2.891 .97 90 3160 7920 39 48 179 188 0 4886 150 4736 2.836 5068 4918 .353 2.791 1.504 1.481
11 11571 8880 166 150 11405 8730 12104 9431 167 153 11938 9281 0 0 3941 3194 31 26 100 100 100 100 20135 21219 1.306 .765 .777 .756 .75 1.176 120 429 .767 .98 120 3310 7920 38 50 193 205 0 8706 147 8559 .75 9246 9099 1.333 .762 -.414 -.392
12 5132 2098 158 145 4974 1953 5297 2278 160 151 5139 2133 0 0 1819 651 30 58 100 100 100 100 6927 7272 2.547 .393 .415 .396 .395 1.268 80 315 .378 .97 100 3460 7920 39 49 209 219 0 2057 142 1915 .385 2233 2091 2.598 .407 -1.377 -1.297
13 4937 4159 154 145 4783 4014 5079 4297 164 178 4925 4152 0 0 1179 830 81 187 100 100 100 100 8797 9077 1.192 .839 .843 .848 .853 1.179 52 265 .817 .98 90 3600 7910 38 47 223 232 0 4077 142 3935 .823 4213 4071 1.215 .827 -.281 -.275
14 1203 823 159 149 1044 674 1213 893 166 165 1054 744 0 0 395 237 72 147 100 98 100 88 1718 1798 1.549 .646 .706 .646 .63 1.326 80 331 .623 .95 100 3750 7920 39 49 238 248 0 807 146 661 .633 875 729 1.58 .692 -.66 -.531
15 8595 6059 157 148 8438 5911 9015 6350 159 147 8858 6202 0 0 2439 1492 28 27 100 100 100 100 14349 15060 1.428 .701 .7 .708 .716 1.158 80 378 .685 .98 110 3890 7920 38 49 251 262 0 5940 145 5795 .687 6225 6080 1.456 .686 -.542 -.543
16 7570 7811 155 144 7415 7667 7258 8096 155 146 7103 7952 0 0 2270 1860 29 32 100 100 100 100 15082 15055 .967 1.034 1.12 1.049 1.04 1.179 80 346 1.008 .98 100 4040 7920 39 49 267 277 0 7658 141 7517 1.014 7937 7796 .986 1.098 .02 .134
17 1148 1346 153 141 995 1205 1184 1361 153 144 1031 1220 0 0 274 228 27 33 100 100 100 100 2200 2251 .826 1.211 1.183 1.239 1.243 1.172 52 289 1.157 .97 90 4180 7920 39 48 281 290 0 1320 138 1181 1.187 1334 1196 .842 1.16 .248 .214
18 709 676 154 144 555 532 720 681 156 145 566 537 0 0 116 85 26 25 100 100 100 100 1087 1103 1.043 .959 .949 .967 .98 1.198 52 283 .93 .96 90 4330 7920 39 48 296 305 0 663 141 522 .94 668 526 1.064 .93 -.09 -.104
19 3033 3857 152 148 2881 3709 3123 3981 158 152 2971 3833 0 0 726 810 59 70 100 100 100 100 6590 6804 .777 1.287 1.29 1.296 1.3 1.161 120 442 1.271 .98 120 4480 7920 38 50 310 322 0 3781 145 3636 1.262 3903 3758 .792 1.265 .336 .339
20 1105 1808 151 147 954 1661 1124 1922 153 147 973 1775 0 0 232 331 27 27 100 100 100 100 2615 2748 .574 1.741 1.824 1.755 1.736 1.206 52 257 1.722 .96 90 4620 7920 39 48 325 334 0 1773 144 1628 1.707 1884 1740 .586 1.788 .771 .839

Total number of rows: 43008

Table truncated, full table size 9758 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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