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Sample GSM90607 Query DataSets for GSM90607
Status Public on Jan 06, 2006
Title ULL-L-112
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-L-112, ampl. totRNA
Organism Homo sapiens
Characteristics cell type: primary breast carcinoma
ID: ULL-L-112
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/2002-11/35562.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 GPL3114
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 1038 254 230 293 808 -39 1030 256 230 294 800 -37 0 0 280 61 30 51 100 6 100 3 769 763 null null null 1 1 1 32 220 1 .16 70 2150 8310 85 92 64 71 0 518 598 -80 null 522 null null null null null
2 1572 1428 227 295 1345 1133 1671 1438 230 298 1444 1143 0 0 464 456 28 54 100 100 100 100 2478 2587 1.187 .842 .792 1 1 1 52 284 1 .98 80 2300 8310 85 93 79 87 0 2914 602 2312 1.719 2935 2333 .582 1.615 .782 .692
3 8415 6429 236 318 8179 6111 8950 6959 237 318 8714 6641 0 0 2412 2042 29 55 100 100 100 100 14290 15355 1.338 .747 .762 1 1 1 80 402 1 .99 100 2450 8300 83 93 93 103 0 13120 649 12471 1.525 14202 13553 .656 1.555 .609 .637
4 5548 11997 235 329 5313 11668 4911 10597 237 330 4676 10268 0 0 3383 7500 30 51 100 100 100 100 16981 14944 .455 2.196 2.196 1 1 1 52 266 1 .99 80 2590 8300 84 92 108 116 0 24484 671 23812 4.482 21627 20955 .223 4.481 2.164 2.164
5 2923 1446 234 313 2689 1133 3108 1436 235 315 2874 1123 0 0 903 428 30 55 100 100 100 100 3822 3997 2.373 .421 .391 1 1 1 52 280 1 .97 80 2740 8310 85 93 123 131 0 2951 639 2312 .86 2931 2292 1.163 .797 -.218 -.327
6 442 365 237 294 205 71 435 371 237 297 198 77 0 0 52 43 26 47 100 66 100 33 276 275 2.887 .346 .389 1 1 1 12 62 1 .63 40 2880 8300 86 90 139 143 0 745 600 145 .707 757 157 1.415 .794 -.501 -.333
7 508 408 224 299 284 109 534 430 227 297 310 131 0 0 104 89 30 47 96 81 96 62 393 441 2.606 .384 .423 1 1 1 32 164 1 .68 60 3030 8300 85 91 153 159 0 833 610 222 .783 878 267 1.277 .862 -.352 -.214
8 6042 4577 236 307 5806 4270 6076 4814 234 307 5840 4507 0 0 3349 2400 30 48 100 100 100 100 10076 10347 1.36 .735 .772 1 1 1 52 295 1 .99 80 3170 8300 84 92 166 174 0 9341 627 8714 1.501 9824 9198 .666 1.575 .586 .655
9 2907 2829 229 291 2678 2538 2820 3013 231 293 2591 2722 0 0 1767 1570 31 49 100 98 98 98 5216 5313 1.055 .948 1.051 1 1 1 52 296 1 .98 80 3330 8310 85 93 182 190 0 5773 594 5180 1.934 6149 5555 .517 2.144 .952 1.1
10 1080 1558 230 284 850 1274 958 1413 230 284 728 1129 0 0 567 761 31 47 96 100 93 100 2124 1857 .667 1.499 1.551 1 1 1 32 176 1 .98 60 3480 8310 86 92 198 204 0 3180 580 2600 3.059 2884 2304 .327 3.165 1.613 1.662
11 4325 2194 236 302 4089 1892 3976 2088 236 304 3740 1786 0 0 2454 1307 30 49 100 100 100 100 5981 5526 2.161 .463 .478 1 1 1 52 271 1 .98 80 3630 8310 85 93 212 220 0 4478 616 3861 .944 4261 3645 1.059 .975 -.083 -.037
12 3003 793 234 296 2769 497 2729 699 234 301 2495 403 0 0 1571 375 28 48 100 87 100 87 3266 2898 5.571 .179 .162 1 1 1 32 160 1 .95 60 3760 8310 86 92 226 232 0 1618 604 1014 .366 1427 822 2.73 .33 -1.449 -1.601
13 2425 1146 236 301 2189 845 2477 1095 270 310 2241 794 0 0 813 439 190 93 100 96 100 93 3034 3035 2.591 .386 .354 1 1 1 32 214 1 .96 70 3900 8300 84 91 239 246 0 2339 614 1724 .788 2235 1620 1.269 .723 -.344 -.468
14 978 434 239 288 739 146 990 428 237 286 751 140 0 0 126 138 32 47 100 66 100 66 885 891 5.062 .198 .186 1 1 1 12 68 1 .77 40 4050 8310 87 91 256 260 0 886 588 298 .403 873 286 2.48 .38 -1.31 -1.394
15 4674 2186 230 294 4444 1892 4836 2309 231 296 4606 2015 0 0 1629 742 31 49 100 100 100 100 6336 6621 2.349 .426 .437 1 1 1 52 272 1 .98 80 4200 8310 85 93 269 277 0 4461 600 3861 .869 4712 4112 1.151 .893 -.203 -.164
16 3114 2823 227 297 2887 2526 3345 2934 226 298 3118 2637 0 0 1262 1040 28 45 100 100 100 100 5413 5755 1.143 .875 .846 1 1 1 52 316 1 .98 90 4340 8300 83 92 282 291 0 5761 606 5155 1.786 5988 5382 .56 1.726 .836 .787
17 720 1411 228 302 492 1109 744 1406 228 301 516 1104 0 0 303 694 28 44 96 100 94 98 1601 1620 .444 2.254 2.14 1 1 1 52 256 1 .96 80 4480 8300 84 92 297 305 0 2880 616 2263 4.6 2869 2253 .217 4.366 2.202 2.126
18 288 251 228 293 60 -42 266 229 229 294 38 -64 0 0 102 105 30 47 51 19 40 11 18 -26 null null null 1 1 1 52 256 1 .41 80 4630 8300 84 92 312 320 0 512 598 -86 null 467 null null null null null
19 2171 1877 232 298 1939 1579 2358 2014 234 297 2126 1716 0 0 574 435 33 52 100 100 100 100 3518 3842 1.228 .814 .807 1 1 1 52 342 1 .98 90 4770 8300 83 92 325 334 0 3831 608 3222 1.662 4110 3502 .602 1.647 .733 .72
20 889 602 234 278 655 324 896 650 238 275 662 372 0 0 85 96 34 53 100 100 100 100 979 1034 2.022 .495 .562 1 1 1 12 104 1 .87 50 4910 8300 85 90 341 346 0 1229 567 661 1.01 1327 759 .991 1.147 .014 .198

Total number of rows: 43008

Table truncated, full table size 9069 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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