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Sample GSM90601 Query DataSets for GSM90601
Status Public on Jan 06, 2006
Title ULL-L-014
Sample type RNA
 
Channel 1
Source name Stratagene Reference, ampl. totRNA
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-T-014, ampl. totRNA
Organism Homo sapiens
Characteristics cell type: primary breast carcinoma
ID: ULL-T-014
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/2002-04/27432.gif
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 1144 1109 140 162 1004 947 1222 1166 141 163 1082 1004 0 0 312 303 21 29 100 100 100 98 1951 2086 1.06 .943 .928 1 1 1 80 371 1 .97 100 1810 8060 65 75 48 58 0 1087 159 928 .925 1143 984 1.081 .91 -.113 -.137
2 1368 1221 143 165 1225 1056 1413 1276 144 167 1270 1111 0 0 338 362 22 27 100 100 100 100 2281 2381 1.16 .862 .875 1 1 1 80 279 1 .97 100 1950 8060 65 75 62 72 0 1197 162 1035 .845 1251 1089 1.183 .858 -.243 -.222
3 3212 3497 142 165 3070 3332 3340 3818 143 167 3198 3653 0 0 1169 1348 23 30 100 100 100 100 6402 6851 .921 1.085 1.142 1 1 1 120 417 1 .98 120 2090 8060 64 76 75 87 0 3428 162 3267 1.064 3743 3581 .94 1.12 .09 .163
4 7313 8057 147 169 7166 7888 8287 8316 150 169 8140 8147 0 0 3420 3755 27 32 100 100 100 100 15054 16287 .908 1.101 1.001 1 1 1 80 340 1 .98 100 2240 8060 65 75 91 101 0 7899 166 7733 1.079 8153 7987 .927 .981 .11 -.027
5 1699 2016 154 173 1545 1843 1761 2157 157 175 1607 1984 0 0 740 775 29 33 100 100 100 100 3388 3591 .838 1.193 1.235 1 1 1 52 222 1 .97 80 2400 8070 67 75 108 116 0 1976 170 1807 1.169 2115 1945 .855 1.21 .226 .275
6 1356 1472 151 178 1205 1294 1362 1544 151 182 1211 1366 0 0 265 318 24 54 100 100 100 100 2499 2577 .931 1.074 1.128 1 1 1 52 302 1 .97 90 2530 8050 64 73 120 129 0 1443 175 1269 1.053 1514 1339 .95 1.106 .074 .145
7 716 994 151 178 565 816 704 1013 154 183 553 835 0 0 97 120 30 39 100 100 100 100 1381 1388 .692 1.444 1.51 1 1 1 52 289 1 .96 90 2680 8060 65 74 135 144 0 975 175 800 1.416 993 819 .706 1.48 .502 .566
8 6127 5018 156 191 5971 4827 6604 5479 190 217 6448 5288 0 0 1249 1408 88 95 100 100 100 100 10798 11736 1.237 .808 .82 1 1 1 52 311 1 .97 90 2810 8050 64 73 148 157 0 4920 187 4732 .793 5372 5184 1.262 .804 -.335 -.315
9 2934 3709 189 248 2745 3461 3030 3848 214 263 2841 3600 0 0 446 750 68 100 100 100 100 100 6206 6441 .793 1.261 1.267 1 1 1 52 282 1 .98 80 2970 8050 65 73 165 173 0 3636 243 3393 1.236 3773 3529 .809 1.242 .306 .313
10 1326 2396 182 218 1144 2178 1378 2574 202 220 1196 2356 0 0 375 566 60 43 100 100 100 100 3322 3552 .525 1.904 1.97 1 1 1 52 231 1 .98 80 3120 8060 66 74 180 188 0 2349 214 2135 1.867 2524 2310 .536 1.931 .9 .95
11 4866 4657 167 194 4699 4463 4974 4732 181 199 4807 4538 0 0 596 687 58 44 100 100 100 100 9162 9345 1.053 .95 .944 1 1 1 80 373 1 .98 110 3260 8060 64 75 192 203 0 4566 190 4375 .931 4639 4449 1.074 .926 -.103 -.112
12 2717 1328 163 195 2554 1133 2904 1358 174 200 2741 1163 0 0 516 260 46 45 100 100 100 100 3687 3904 2.254 .444 .424 1 1 1 52 300 1 .96 90 3400 8050 64 73 207 216 0 1302 191 1111 .435 1331 1140 2.299 .416 -1.201 -1.265
13 2669 2577 181 213 2488 2364 2743 2777 203 236 2562 2564 0 0 363 496 72 106 100 100 100 100 4852 5126 1.052 .95 1.001 1 1 1 52 312 1 .97 90 3550 8050 64 73 222 231 0 2526 209 2318 .932 2723 2514 1.074 .981 -.102 -.027
14 921 778 182 213 739 565 910 761 210 233 728 548 0 0 151 131 81 85 100 100 100 100 1304 1276 1.308 .765 .753 1 1 1 52 243 1 .94 80 3700 8060 66 74 238 246 0 763 209 554 .75 746 537 1.334 .738 -.416 -.438
15 4971 4844 170 218 4801 4626 5351 5147 194 249 5181 4929 0 0 1566 1308 69 169 100 100 100 100 9427 10110 1.038 .964 .951 1 1 1 80 346 1 .98 100 3850 8060 65 75 252 262 0 4749 214 4535 .945 5046 4832 1.059 .933 -.082 -.101
16 5081 7291 175 223 4906 7068 5208 7549 190 280 5033 7326 0 0 764 1147 68 286 100 100 100 100 11974 12359 .694 1.441 1.456 1 1 1 52 284 1 .97 90 3980 8050 64 73 265 274 0 7148 219 6929 1.412 7401 7182 .708 1.427 .498 .513
17 580 1013 173 223 407 790 578 1015 181 235 405 792 0 0 88 137 53 132 100 100 100 100 1197 1197 .515 1.941 1.956 1 1 1 52 335 1 .93 90 4140 8060 65 74 281 290 0 993 219 775 1.903 995 776 .525 1.917 .928 .939
18 474 542 219 259 255 283 478 533 236 284 259 274 0 0 57 84 79 96 96 100 96 84 538 533 .901 1.11 1.058 1 1 1 32 191 1 .78 70 4290 8070 67 74 297 304 0 531 254 277 1.088 523 269 .919 1.037 .122 .053
19 1771 2338 179 229 1592 2109 1812 2354 229 287 1633 2125 0 0 240 265 104 129 100 100 100 100 3701 3758 .755 1.325 1.301 1 1 1 80 402 1 .96 110 4430 8060 64 75 309 320 0 2292 225 2068 1.299 2308 2083 .77 1.276 .377 .351
20 789 1071 228 324 561 747 680 978 371 435 452 654 0 0 315 354 278 273 86 92 36 69 1308 1106 .751 1.332 1.447 1 1 1 52 243 1 .93 80 4570 8050 65 73 325 333 -50 1050 318 732 1.305 959 641 .766 1.419 .385 .504

Total number of rows: 43008

Table truncated, full table size 9334 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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