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Sample GSM90564 Query DataSets for GSM90564
Status Public on Jan 06, 2006
Title ULL-L-024
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-024, ampl. totRNA
Organism Homo sapiens
Characteristics cell type: primary breast carcinoma
ID: ULL-T-024
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/2002-04/27245.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
1 831 521 110 100 721 421 831 500 109 99 721 400 0 0 159 95 24 23 100 100 100 100 1142 1121 1.713 .584 .555 1 1 1 52 356 1 .91 90 1710 8000 99 108 62 71 0 734 141 593 .822 704 563 1.216 .781 -.282 -.356
2 1592 726 106 95 1486 631 1625 730 108 97 1519 635 0 0 249 119 21 23 100 100 100 100 2117 2154 2.355 .425 .418 1 1 1 52 324 1 .95 90 1860 8000 99 108 77 86 0 1023 134 889 .598 1028 894 1.672 .589 -.742 -.764
3 2568 8256 109 95 2459 8161 2468 7938 109 97 2359 7843 0 0 538 1833 21 26 100 100 100 100 10620 10202 .301 3.319 3.325 1 1 1 80 408 1 .95 110 2020 8010 99 110 92 103 0 11628 134 11494 4.674 11180 11046 .214 4.683 2.225 2.227
4 8382 12319 113 99 8269 12220 8556 12683 114 101 8443 12584 0 0 3321 5728 20 24 100 100 100 100 20489 21027 .677 1.478 1.49 1 1 1 52 296 1 .94 90 2150 8000 99 108 106 115 0 17351 139 17211 2.081 17863 17724 .48 2.099 1.058 1.07
5 1976 2427 113 93 1863 2334 2076 2500 115 95 1963 2407 0 0 867 898 19 21 100 100 100 100 4197 4370 .798 1.253 1.226 1 1 1 52 250 1 .94 80 2310 8000 100 108 123 131 0 3418 131 3287 1.765 3521 3390 .567 1.727 .819 .788
6 875 635 112 91 763 544 929 685 113 93 817 594 0 0 244 149 20 20 100 100 100 100 1307 1411 1.403 .713 .727 1 1 1 52 300 1 .92 90 2440 8000 99 108 135 144 0 894 128 766 1.004 965 837 .996 1.024 .006 .034
7 634 727 109 94 525 633 631 712 111 96 522 618 0 0 138 122 21 30 100 100 100 100 1158 1140 .829 1.206 1.184 1 1 1 52 312 1 .92 90 2590 8000 99 108 150 159 0 1024 132 892 1.698 1003 870 .589 1.667 .764 .738
8 5462 6091 110 92 5352 5999 5775 6231 110 95 5665 6139 0 0 1555 1722 19 21 100 100 100 100 11351 11804 .892 1.121 1.084 1 1 1 52 300 1 .94 90 2730 8000 99 108 164 173 0 8579 130 8449 1.579 8776 8646 .633 1.526 .659 .61
9 3066 3055 108 92 2958 2963 3092 2982 109 91 2984 2890 0 0 859 953 20 20 100 100 100 100 5921 5874 .998 1.002 .968 1 1 1 52 313 1 .94 90 2880 8000 99 108 179 188 0 4303 130 4173 1.411 4200 4070 .709 1.364 .497 .448
10 932 1656 104 88 828 1568 961 1769 106 89 857 1681 0 0 295 534 19 19 100 100 100 100 2396 2538 .528 1.894 1.961 1 1 1 52 227 1 .93 80 3030 8000 100 108 195 203 0 2332 124 2208 2.667 2492 2368 .375 2.763 1.415 1.466
11 4783 4231 102 83 4681 4148 5545 4484 103 86 5443 4401 0 0 2108 1835 19 20 100 100 100 100 8829 9844 1.128 .886 .809 1 1 1 120 449 1 .94 120 3180 8000 98 110 208 220 0 5959 117 5842 1.248 6315 6199 .801 1.139 .32 .188
12 2743 2130 100 86 2643 2044 2811 2187 102 87 2711 2101 0 0 699 453 18 20 100 100 100 100 4687 4812 1.293 .773 .775 1 1 1 52 268 1 .93 90 3320 7990 98 107 223 232 0 3000 121 2879 1.089 3080 2959 .918 1.092 .123 .126
13 2534 1666 100 87 2434 1579 2727 1728 102 90 2627 1641 0 0 773 390 20 26 100 100 100 100 4013 4268 1.541 .649 .625 1 1 1 52 300 1 .92 90 3460 7990 98 107 237 246 0 2346 123 2224 .914 2434 2311 1.094 .88 -.13 -.185
14 654 388 99 88 555 300 680 371 101 89 581 283 0 0 140 70 19 23 100 100 100 100 855 864 1.85 .541 .487 1 1 1 52 302 1 .88 90 3610 8000 99 108 252 261 0 546 124 423 .761 523 399 1.314 .686 -.393 -.544
15 4189 3216 101 88 4088 3128 4383 3245 102 108 4282 3157 0 0 1369 703 21 162 100 100 100 100 7216 7439 1.307 .765 .737 1 1 1 52 302 1 .92 90 3750 7990 98 107 266 275 0 4530 124 4406 1.078 4570 4446 .928 1.038 .108 .054
16 3365 3258 97 84 3268 3174 3773 3354 98 94 3676 3270 0 0 1346 1138 18 87 100 100 100 100 6442 6946 1.03 .971 .89 1 1 1 80 351 1 .9 100 3900 8000 99 109 281 291 0 4589 118 4470 1.368 4724 4606 .731 1.253 .452 .325
17 662 819 97 83 565 736 679 869 99 85 582 786 0 0 184 190 17 21 100 100 96 100 1301 1368 .768 1.303 1.351 1 1 1 52 288 1 .91 90 4040 7990 98 107 295 304 0 1154 117 1037 1.835 1224 1107 .545 1.902 .876 .928
18 284 193 99 88 185 105 295 191 100 89 196 103 0 0 69 48 18 20 96 98 96 88 290 299 1.762 .568 .526 1 1 1 52 264 1 .78 80 4190 7990 99 107 311 319 0 272 124 148 .799 269 145 1.251 .74 -.323 -.434
19 1861 2211 101 88 1760 2123 1827 2212 102 89 1726 2124 0 0 465 459 20 20 100 100 100 100 3883 3850 .829 1.206 1.231 1 1 1 80 403 1 .92 110 4340 8000 98 109 324 335 0 3114 124 2990 1.699 3115 2992 .589 1.733 .765 .793
20 432 539 104 88 328 451 416 552 105 90 312 464 0 0 91 88 19 20 100 100 100 100 779 776 .727 1.375 1.487 1 1 1 52 278 1 .93 90 4490 7990 98 107 340 349 0 759 124 635 1.937 777 654 .516 2.095 .954 1.067

Total number of rows: 43008

Table truncated, full table size 9066 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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