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Sample GSM73720 Query DataSets for GSM73720
Status Public on Sep 10, 2005
Title BC-A
Sample type RNA
 
Channel 1
Source name CR2 reference
Organism Homo sapiens
Characteristics CR2 reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BC-A normal
Organism Homo sapiens
Characteristics BC-A normal
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2278.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Sep 09, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL180
Series (5)
GSE3193 Breast Tumor Clinical Implications
GSE3281 Breast Cancer aCGH
GSE4268 Breast and ovarian carcinoma

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1D_MEAN The mean feature pixel intensity with the median background subtracted (channel 1).; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity with the median background subtracted (channel 2).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEAN Mean intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN Mean intensities of background pixels of Cy5.; Type: integer; Scale: linear_scale; 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
PIX_RAT2_MEDIAN Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.; Type: float; Scale: linear_scale
TOT_SPIX Count of the number of pixels in the spot.; Type: integer; Scale: linear_scale
TOT_BPIX 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
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 User defined spot flag (default 0).; 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
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
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE 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

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1B_MEAN CH2B_MEAN PERGTBCH1I_1SD PERGTBCH2I_1SD PIX_RAT2_MEDIAN TOT_SPIX TOT_BPIX REGR CORR TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN RAT1N_MEAN VALUE UNF_VALUE
1 2683 6461 1574 4453 1109 2008 1849 4690 40 34 1.972 225 1001 1.157 .854 115 132 56 73 0 5682 3916 1766 1.592 .628 .671 .671
2 3060 5564 1668 4702 1392 862 2153 5025 50 11 .75 225 746 .647 .88 114 131 73 90 0 4894 4135 758 .545 1.836 -.877 -.877
3 2360 3947 1658 4627 702 null 1926 4798 32 0 1.751 225 721 .284 .32 114 131 91 108 0 3471 4069 -598 null null null null
4 2328 3911 1666 4721 662 null 1689 4730 34 0 1.046 225 731 null null 113 130 108 125 0 3440 4152 -712 null null null null
5 4564 4280 1742 4899 2822 null 1831 4999 57 2 .699 225 746 null null 112 129 126 143 0 3764 4309 -544 null null null null
6 3743 6036 1753 4903 1990 1133 1847 4984 70 11 .539 225 731 .619 .772 112 129 143 160 0 5309 4312 996 .501 1.997 -.998 -.998
7 1708 4174 1658 4641 50 null 1705 4658 1 0 1.781 225 746 1.232 .522 111 128 161 178 0 3671 4082 -411 null null null null
8 5894 6140 1596 4457 4298 1683 1728 4663 40 31 .438 225 721 .501 .761 111 128 178 195 0 5400 3920 1480 .344 2.904 -1.538 -1.538
9 1605 4017 1527 4263 78 null 1537 4344 7 1 1.244 225 731 .866 .199 110 127 196 213 0 3533 3749 -216 null null null null
10 4999 6933 1477 4061 3522 2872 1493 4085 43 36 .869 225 746 .751 .959 109 126 213 230 0 6098 3572 2526 .717 1.394 -.48 -.48
11 3666 5902 1437 3882 2229 2020 1585 4223 65 45 .939 225 731 1.027 .867 109 126 231 248 0 5191 3414 1777 .797 1.255 -.327 -.327
12 2535 4017 1395 3804 1140 213 1711 4561 36 5 .187 225 746 1.205 .757 108 125 248 265 0 3533 3346 187 .164 6.085 -2.605 -2.605
13 1503 3772 1349 3707 154 65 1606 4306 5 1 1.955 225 721 2.017 .919 108 125 266 283 0 3317 3260 57 .371 2.694 -1.43 -1.43
14 1834 3943 1320 3650 514 293 1321 3600 37 7 .959 225 743 .959 .724 107 124 283 300 0 3468 3210 258 .501 1.995 -.996 -.996
15 11585 6620 1295 3542 10290 3078 1308 3490 64 43 .327 225 746 .325 .952 106 123 301 318 0 5822 3115 2707 .263 3.801 -1.926 -1.926
16 2365 2810 1268 3364 1097 null 1307 3375 59 2 .398 225 733 null null 106 123 318 335 0 2471 2959 -487 null null null null
17 1901 3675 1208 3218 693 457 1256 3232 42 11 .763 225 746 .757 .766 105 122 336 353 0 3232 2830 402 .58 1.724 -.786 -.786
18 1234 3336 1193 3138 41 198 1241 3142 4 4 1.935 225 724 .919 .526 105 122 353 370 0 2934 2760 174 4.247 .235 2.087 2.087
19 4311 6533 1103 2921 3208 3612 1131 2765 81 60 1.179 225 731 1.202 .941 104 121 371 388 0 5746 2569 3177 .99 1.01 -.014 -.014
20 2073 3197 1081 2853 992 344 1099 2666 48 16 .733 225 748 .888 .847 103 120 388 405 0 2812 2509 303 .305 3.279 -1.713 -1.713

Total number of rows: 9216

Table truncated, full table size 1128 Kbytes.




Supplementary data files not provided
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